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  • Journal article
    Li X, Krishnan L, Cherepanov P, Engelman Aet al., 2011,

    Structural biology of retroviral DNA integration

    , VIROLOGY, Vol: 411, Pages: 194-205, ISSN: 0042-6822
  • Journal article
    Sage JT, Zhang Y, McGeehan J, Ravelli RBG, Weik M, Thor JJVet al., 2011,

    Infrared protein crystallography

    , Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol: 1841, Pages: 760-777

    We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO2. Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
  • Journal article
    Luther PK, Vydyanath A, 2011,

    Myosin binding protein-C: an essential protein in skeletal and cardiac muscle

    , JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY, Vol: 31, Pages: 303-305, ISSN: 0142-4319
  • Journal article
    Hussain S-A, Carafoli F, Hohenester E, 2011,

    Determinants of laminin polymerization revealed by the structure of the α5 chain amino-terminal region

    , EMBO REPORTS, Vol: 12, Pages: 276-282, ISSN: 1469-221X
  • Journal article
    Hachani A, Lossi NS, Hamilton A, Jones C, Bleves S, Albesa-Jove D, Filloux Aet al., 2011,

    Type VI Secretion System in Pseudomonas aeruginosa: Secretion and Multimerization of VgrG Proteins

    , Journal of Biological Chemistry, Vol: 286, ISSN: 1083-351X

    Pseudomonas aeruginosa is a Gram-negative bacterium causing chronic infections in cystic fibrosis patients. Such infections are associated with an active type VI secretion system (T6SS), which consists of about 15 conserved components, including the AAA+ ATPase, ClpV. The T6SS secretes two categories of proteins, VgrG and Hcp. Hcp is structurally similar to a phage tail tube component, whereas VgrG proteins show similarity to the puncturing device at the tip of the phage tube. In P. aeruginosa, three T6SSs are known. The expression of H1-T6SS genes is controlled by the RetS sensor. Here, 10 vgrG genes were identified in the PAO1 genome, among which three are co-regulated with H1-T6SS, namely vgrG1a/b/c. Whereas VgrG1a and VgrG1c were secreted in a ClpV1-dependent manner, secretion of VgrG1b was ClpV1-independent. We show that VgrG1a and VgrG1c form multimers, which confirmed the VgrG model predicting trimers similar to the tail spike. We demonstrate that Hcp1 secretion requires either VgrG1a or VgrG1c, which may act independently to puncture the bacterial envelope and give Hcp1 access to the surface. VgrG1b is not required for Hcp1 secretion. Thus, VgrG1b does not require H1-T6SS for secretion nor does H1-T6SS require VgrG1b for its function. Finally, we show that VgrG proteins are required for secretion of a genuine H1-T6SS substrate, Tse3. Our results demonstrate that VgrG proteins are not only secreted components but are essential for secretion of other T6SS substrates. Overall, we emphasize variability in behavior of three P. aeruginosa VgrGs, suggesting that, although very similar, distinct VgrGs achieve specific functions.
  • Journal article
    Maruf MUATBELDPRNMCS-SAHCMMGRGJMWAICFEDALHP, 2011,

    Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response

    , EMBO J, Vol: 30, Pages: 894-905
  • Journal article
    Bush M, Ghosh T, Tucker N, Zhang X, Dixon Ret al., 2011,

    Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification

    , BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 39, Pages: 289-293, ISSN: 0300-5127
  • Journal article
    Woermann ME, Corrigan RM, Simpson PJ, Matthews SJ, Gruendling Aet al., 2011,

    Enzymatic activities and functional interdependencies of <i>Bacillus subtilis</i> lipoteichoic acid synthesis enzymes

    , MOLECULAR MICROBIOLOGY, Vol: 79, Pages: 566-583, ISSN: 0950-382X
  • Conference paper
    Cota E, 2011,

    Als adhesins - Structural basis for the broad specificity to host-cell ligands by Candida albicans

    , Host-fungal interactions: pathogenicity versus immunity, Pages: 149-151

    Als (agglutinin-like sequence) glycoproteins have been associated with binding of host-cell surface proteins and small peptides of random sequence, the formation of biofilms and amyloid fibers. High-resolution structures of N-terminal Als domains show that ligand recognition relies on a motif capable of binding flexible C termini of peptides in extended conformation. These data establish NT-Als adhesins as a separate family of peptide-binding proteins and an unexpected adhesion system for primary, widespread protein–protein interactions at the Candida/host-cell interface. The new structural information also provides potential templates for the design of novel antifungals.
  • Journal article
    Sonoda Y, Newstead S, Hu N-J, Alguel Y, Nji E, Beis K, Yashiro S, Lee C, Leung J, Cameron AD, Byrne B, Iwata S, Drew Det al., 2011,

    Benchmarking Membrane Protein Detergent Stability for Improving Throughput of High-Resolution X-ray Structures

    , STRUCTURE, Vol: 19, Pages: 17-25, ISSN: 0969-2126
  • Journal article
    Klein BJ, Bose D, Baker KJ, Yusoff ZM, Zhang X, Murakami KSet al., 2011,

    RNA polymerase and transcription elongation factor Spt4/5 complex structure

    , Proc Natl Acad Sci U S A., Vol: 108(2), Pages: 546-550
  • Journal article
    Salgado PS, Taylor JD, Cota E, Matthews SJet al., 2011,

    Extending the usability of the phasing power of diselenide bonds: SeCys SAD phasing of CsgC using a non-auxotrophic strain

    , ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, Vol: 67, Pages: 8-13, ISSN: 2059-7983
  • Journal article
    Ellis T, Adie T, Baldwin GS, 2011,

    DNA assembly for synthetic biology: from parts to pathways and beyond

    , INTEGRATIVE BIOLOGY, Vol: 3, Pages: 109-118, ISSN: 1757-9694
  • Journal article
    Jovanovic M, Burrows PC, Bose D, Camara B, Wiesler S, Zhang X, Wigneshweraraj S, Weinzierl RO, Buck Met al., 2011,

    Activity map of the Escherichia coli RNA polymerase bridge helix

    , J Biol Chem, Vol: 286, Pages: 14469-14479, ISSN: 1083-351X

    Transcription, the synthesis of RNA from a DNA template, is performed by multisubunit RNA polymerases (RNAPs) in all cellular organisms. The bridge helix (BH) is a distinct feature of all multisubunit RNAPs and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and RNA and DNA binding. Because the BH has been captured in both kinked and straight conformations in different crystals structures of RNAP, recently supported by molecular dynamics studies, it has been proposed that cycling between these conformations is an integral part of the nucleotide addition cycle. To further evaluate the role of the BH, we conducted systematic alanine scanning mutagenesis of the Escherichia coli RNAP BH to determine its contributions to activities required for transcription. Combining our data with an atomic model of E. coli RNAP, we suggest that alterations in the interactions between the BH and (i) the trigger loop, (ii) fork loop 2, and (iii) switch 2 can help explain the observed changes in RNAP functionality associated with some of the BH variants. Additionally, we show that extensive defects in E. coli RNAP functionality depend upon a single previously not studied lysine residue (Lys-781) that is strictly conserved in all bacteria. It appears that direct interactions made by the BH with other conserved features of RNAP are lost in some of the E. coli alanine substitution variants, which we infer results in conformational changes in RNAP that modify RNAP functionality.
  • Journal article
    Burgess SJ, Tamburic B, Zemichael F, Hellgardt K, Nixon PJet al., 2011,

    Solar-Driven Hydrogen Production in Green Algae

    , ADVANCES IN APPLIED MICROBIOLOGY, VOL 75, Vol: 75, Pages: 71-110, ISSN: 0065-2164
  • Book chapter
    Thor JJV, 2011,

    Photoconversion of the Green Fluorescent Protein and Related Proteins

    , Springer Series on Fluorescence, Editors: Wolfbeis, Hof

    This review focuses on the mechanistic details of photochromic reactions of the green fluorescent protein (GFP) and also of its mutant derivatives and related fluorescent proteins. A number of distinct photochromic processes have so far been identified that have entirely different photochemical and chemical basis, which will be reviewed. In addition to bright fluorescence, the GFP from the jellyfish Aequorea victoria undergoes photochromic transformation with blue or UV illumination. The associated change in electronic absorption provides a spectroscopic contrast that can be used in fluorescence microscopy application to tag and track the movement of populations that are photoconverted. Key to the successful use of photoconversion for such microscopy experiments is in fact the relatively low quantum yield of the irreversible process. In the wild-type GFP, photoconversion is triggered by light-induced electron transfer from the buried anionic carboxylate of Glu222 to the optically excited protonated chromophore. An unstable carboxylate radical subsequently cleaves off a CO2 molecule in a “Kolbe” type reaction that has been trapped in a partially oriented site near the chromophore-binding site at 100K, as observed by low-temperature X-ray crystallography and cryo-infrared crystallography. Structural intermediates in the subsequent relaxation pathway involve motion of CO2, amino acids and H-bonded waters both in the chromophore vicinity and at longer range. This review provides an overview of the molecular characterisation using structural and spectroscopy methods of this photoconversion reaction of GFP. In addition, the mechanisms of photochromic reactions of mutants of GFP and related fluorescent proteins will be summarised and discussed. These include the cis–trans isomerisation and protonation changes in Dronpa, asFP595 and IrisFP and related proteins, light-induced maturation in aceGFPL, and photoinduced beta-elimination and backbone cleavage tha
  • Journal article
    Jefferson AE, Williams DR, Heng JYY, 2011,

    Computing the Surface Energy Distributions of Heterogeneous Crystalline Powders

    , JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY, Vol: 25, Pages: 339-355, ISSN: 0169-4243
  • Journal article
    Ivanov AP, Instuli E, McGilvery C, Baldwin G, McComb DW, Albrecht T, Edel JBet al., 2010,

    DNA tunneling detector embedded in a nanopore

    , Nano Letters, Vol: 11, Pages: 279-285, ISSN: 1530-6992

    We report on the fabrication and characterization of a DNA nanopore detector with integrated tunneling electrodes. Functional tunneling devices were identified by tunneling spectroscopy in different solvents and then used in proof-of-principle experiments demonstrating, for the first time, concurrent tunneling detection and ionic current detection of DNA molecules in a nanopore platform. This is an important step toward ultrafast DNA sequencing by tunneling.
  • Journal article
    Kulkarni MV, Tettamanzi MC, Murphy JW, Keeler C, Myszka DG, Chayen NE, Lolis EJ, Hodsdon MEet al., 2010,

    Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation

    , JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 285, Pages: 38524-38533
  • Journal article
    Coulon C, Vinogradov E, Filloux A, Sadovskaya Iet al., 2010,

    Chemical analysis of cellular and extracellular carbohydrates of a biofilm-forming strain pseudomonas aeruginosa PA14

    , PLoS ONE, Vol: 5, ISSN: 1932-6203

    BackgroundPseudomonas aeruginosa is a Gram-negative bacterium and an opportunistic pathogen, which causes persisting life-threatening infections in cystic fibrosis (CF) patients. Biofilm mode of growth facilitates its survival in a variety of environments. Most P. aeruginosa isolates, including the non-mucoid laboratory strain PA14, are able to form a thick pellicle, which results in a surface-associated biofilm at the air-liquid (A–L) interface in standing liquid cultures. Exopolysaccharides (EPS) are considered as key components in the formation of this biofilm pellicle. In the non-mucoid P. aeruginosa strain PA14, the “scaffolding” polysaccharides of the biofilm matrix, and the molecules responsible for the structural integrity of rigid A–L biofilm have not been identified. Moreover, the role of LPS in this process is unclear, and the chemical structure of the LPS O-antigen of PA14 has not yet been elucidated.Principal FindingsIn the present work we carried out a systematic analysis of cellular and extracellular (EC) carbohydrates of P. aeruginosa PA14. We also elucidated the chemical structure of the LPS O-antigen by chemical methods and 2-D NMR spectroscopy. Our results showed that it is composed of linear trisaccharide repeating units, identical to those described for P. aeruginosa Lanýi type O:2a,c (Lanýi-Bergman O-serogroup 10a, 10c; IATS serotype 19) and having the following structure: -4)-α-L-GalNAcA-(1–3)-α-D-QuiNAc-(1–3)- α-L-Rha-(1-. Furthermore, an EC O-antigen polysaccharide (EC O-PS) and the glycerol-phosphorylated cyclic β-(1,3)-glucans were identified in the culture supernatant of PA14, grown statically in minimal medium. Finally, the extracellular matrix of the thick biofilm formed at the A-L interface contained, in addition to eDNA, important quantities (at least ∼20% of dry weight) of LPS-like material.ConclusionsWe characterized the chemical structure of the LPS O-anti
  • Journal article
    Alguel Y, Lu D, Quade N, Sauter S, Zhang Xet al., 2010,

    Crystal structure of MexZ, a key repressor responsible for antibiotic resistance in <i>Pseudomonas aeruginosa</i>

    , JOURNAL OF STRUCTURAL BIOLOGY, Vol: 172, Pages: 305-310, ISSN: 1047-8477
  • Journal article
    Low HH, Loewe J, 2010,

    Dynamin architecture - from monomer to polymer

    , CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 20, Pages: 791-798, ISSN: 0959-440X
  • Journal article
    Gianni S, Ivarsson Y, De Simone A, Travaglini-Allocatelli C, Brunori M, Vendruscolo Met al., 2010,

    Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain

    , NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 17, Pages: 1431-U57, ISSN: 1545-9993
  • Journal article
    Bushell SR, Lou H, Wallat GD, Beis K, Whitfield C, Naismith JHet al., 2010,

    Crystallization and preliminary diffraction analysis of Wzi, a member of the capsule export and assembly pathway in <i>Escherichia coli</i>

    , ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, Vol: 66, Pages: 1621-1625
  • Journal article
    Bleves S, Viarre V, Salacha R, Michel GPF, Filloux A, Voulhoux Ret al., 2010,

    Protein secretion systems in <i>Pseudomonas aeruginosa</i>: A wealth of pathogenic weapons

    , INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, Vol: 300, Pages: 534-543, ISSN: 1438-4221
  • Journal article
    Bebeacua C, Bron P, Lai L, Vegge CS, Brondsted L, Spinelli S, Campanacci V, Veesler D, van Heel M, Cambillau Cet al., 2010,

    Structure and Molecular Assignment of Lactococcal Phage TP901-1 Baseplate

    , JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 285, Pages: 39079-39086, ISSN: 0021-9258
  • Journal article
    Bhavsar PK, Brand NJ, Felkin LE, Luther PK, Cullen ME, Yacoub MH, Barton PJRet al., 2010,

    Clenbuterol Induces Cardiac Myocyte Hypertrophy via Paracrine Signalling and Fibroblast-derived IGF-1

    , JOURNAL OF CARDIOVASCULAR TRANSLATIONAL RESEARCH, Vol: 3, Pages: 688-695, ISSN: 1937-5387
  • Journal article
    Heathcote DA, Patel H, Kroll SH, Hazel P, Periyasamy M, Alikian M, Kannegnti SK, Jogalekar AS, Scheiper B, Barbazanges M, Blum A, Brackow J, Siwicka A, Pace RD, Fuchter MJ, Snyder JP, Liotta DC, Freemont PS, Aboagye EO, Coombes RC, Barrett AG, Ali Set al., 2010,

    A novel pyrazolo[1,5-a]pyrimidine is a potent inhibitor of cyclin-dependent protein kinases 1, 2, and 9, which demonstrates antitumor effects in human tumor xenografts following oral administration

    , J Med Chem, Vol: 53, Pages: 8508-8522

    Cyclin-dependent protein kinases (CDKs) are central to the appropriate regulation of cell proliferation, apoptosis, and gene expression. Abnormalities in CDK activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Here, we report the identification of a pyrazolo[1,5-a]pyrimidine derived compound, 4k (BS-194), as a selective and potent CDK inhibitor, which inhibits CDK2, CDK1, CDK5, CDK7, and CDK9 (IC= 3, 30, 30, 250, and 90 nmol/L, respectively). Cell-based studies showed inhibition of the phosphorylation of CDK substrates, Rb and the RNA polymerase II C-terminal domain, down-regulation of cyclins A, E, and D1, and cell cycle block in the S and G/M phases. Consistent with these findings, 4k demonstrated potent antiproliferative activity in 60 cancer cell lines tested (mean GI= 280 nmol/L). Pharmacokinetic studies showed that 4k is orally bioavailable, with an elimination half-life of 178 min following oral dosing in mice. When administered at a concentration of 25 mg/kg orally, 4k inhibited human tumor xenografts and suppressed CDK substrate phosphorylation. These findings identify 4k as a novel, potent CDK selective inhibitor with potential for oral delivery in cancer patients.
  • Journal article
    Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov Pet al., 2010,

    Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance

    , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 20057-20062, ISSN: 0027-8424
  • Journal article
    Lu D, Fillet S, Meng C, Alguel Y, Kloppsteck P, Bergeron J, Krell T, Gallegos M-T, Ramos J, Zhang Xet al., 2010,

    Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators

    , GENES & DEVELOPMENT, Vol: 24, Pages: 2556-2565, ISSN: 0890-9369

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