Nicolas Joly

Summary

Affiliation: Imperial College
Country: UK

Publications

  1. pmc Engineered interfaces of an AAA+ ATPase reveal a new nucleotide-dependent coordination mechanism
    Nicolas Joly
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Biol Chem 285:15178-86. 2010
  2. pmc Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting
    Patricia C Burrows
    Division of Biology, Department of Life Sciences, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 387:306-19. 2009
  3. ncbi Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    Mol Microbiol 66:583-95. 2007
  4. ncbi Determination of the self-association residues within a homomeric and a heteromeric AAA+ enhancer binding protein
    Edward Lawton
    Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK
    J Mol Biol 426:1692-710. 2014
  5. doi Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA+ ring ATPase
    Jorg Schumacher
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 381:1-12. 2008
  6. pmc Comparative analysis of activator-Esigma54 complexes formed with nucleotide-metal fluoride analogues
    Patricia C Burrows
    Department of Life Sciences, Division of Biology, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    Nucleic Acids Res 37:5138-50. 2009
  7. pmc A key hydrophobic patch identified in an AAA⁺ protein essential for its in trans inhibitory regulation
    Nan Zhang
    Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK
    J Mol Biol 425:2656-69. 2013
  8. ncbi Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase
    Jorg Schumacher
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Biol Chem 282:9825-33. 2007
  9. pmc The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins
    Nan Zhang
    Division of Biology, Sir Alexander Fleming Building, and Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College London, London SW7 2AZ, UK
    Nucleic Acids Res 37:5981-92. 2009
  10. doi Coupling AAA protein function to regulated gene expression
    Nicolas Joly
    Division of Biology, Imperial College London, London, SW7 2AZ, UK
    Biochim Biophys Acta 1823:108-16. 2012

Detail Information

Publications24

  1. pmc Engineered interfaces of an AAA+ ATPase reveal a new nucleotide-dependent coordination mechanism
    Nicolas Joly
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Biol Chem 285:15178-86. 2010
    ..As the structural AAA(+) core is conserved, we propose that the functional networks established here could serve as a template to identify similar residue pairs in other AAA(+) proteins...
  2. pmc Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting
    Patricia C Burrows
    Division of Biology, Department of Life Sciences, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 387:306-19. 2009
    ....
  3. ncbi Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    Mol Microbiol 66:583-95. 2007
    ..In addition, we show the importance of this glutamate residue in sigma(54).DNA conformation sensing, permitting the identification of new intermediate stages within the transcription activation pathway...
  4. ncbi Determination of the self-association residues within a homomeric and a heteromeric AAA+ enhancer binding protein
    Edward Lawton
    Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK
    J Mol Biol 426:1692-710. 2014
    ....
  5. doi Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA+ ring ATPase
    Jorg Schumacher
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 381:1-12. 2008
    ..Homotropic coordination is functionally important to remodel the sigma(54) promoter. We propose a structural symmetry-based model for homotropic control in the AAA(+) characteristic ring architecture...
  6. pmc Comparative analysis of activator-Esigma54 complexes formed with nucleotide-metal fluoride analogues
    Patricia C Burrows
    Department of Life Sciences, Division of Biology, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    Nucleic Acids Res 37:5138-50. 2009
    ....
  7. pmc A key hydrophobic patch identified in an AAA⁺ protein essential for its in trans inhibitory regulation
    Nan Zhang
    Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK
    J Mol Biol 425:2656-69. 2013
    ..By structural modelling, we propose that PspA binds to PspF via its first two helical domains. After PspF binding-induced conformational changes, PspA may then share structural similarities with a bEBP regulatory domain...
  8. ncbi Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase
    Jorg Schumacher
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Biol Chem 282:9825-33. 2007
    ..We propose that hydrolysis is relayed via Thr(148) to loop 2 creating motions that provide mechanical force to the GAFTGA loop 1 that contacts sigma(54)...
  9. pmc The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins
    Nan Zhang
    Division of Biology, Sir Alexander Fleming Building, and Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College London, London SW7 2AZ, UK
    Nucleic Acids Res 37:5981-92. 2009
    ..The functionality of F85 is distinct from that of other GAFTGA residues, especially T86 where in contrast to F85 a clean uncoupling phenotype is observed...
  10. doi Coupling AAA protein function to regulated gene expression
    Nicolas Joly
    Division of Biology, Imperial College London, London, SW7 2AZ, UK
    Biochim Biophys Acta 1823:108-16. 2012
    ..These specialised macromolecular machines remodel their substrates through ATP hydrolysis that ultimately leads to transcriptional activation. We will discuss how AAA proteins are specialised for this specific task...
  11. pmc Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
    J Mol Biol 375:1206-11. 2008
    ....
  12. doi An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
    J Biol Chem 283:13725-35. 2008
    ..Such functional organization most likely applies to other AAA+ proteins, including Ltag (simian virus 40), Rep40 (Adeno-associated virus-2), and p97 (Mus musculus) in which the asparagine to Walker B motif relationship is conserved...
  13. ncbi Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, United Kingdom
    J Biol Chem 281:34997-5007. 2006
    ..Esigma54 complex provides clear biochemical evidence for heterogeneous nucleotide occupancy in this AAA+ protein. Based on our data, we propose a stochastic nucleotide binding and a coordinated hydrolysis mechanism in PspF1-275 hexamers...
  14. pmc ATPase site architecture is required for self-assembly and remodeling activity of a hexameric AAA+ transcriptional activator
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    Mol Cell 47:484-90. 2012
    ..Another glutamic acid controls hexamer formation in the presence of nucleotides. Together, these results lead to a "residue-nucleotide" interaction map upon which to base AAA+ core regulation...
  15. doi Visualizing the organization and reorganization of transcription complexes for gene expression
    Patricia C Burrows
    Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, UK
    Biochem Soc Trans 36:776-9. 2008
    ....
  16. pmc A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements
    Nan Zhang
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
    Nucleic Acids Res 40:9139-52. 2012
    ..The mechanistic implications for these multivalent L1 interactions are elaborated in the light of available structures for the bEBP and its target complexes...
  17. pmc A lower-order oligomer form of phage shock protein A (PspA) stably associates with the hexameric AAA(+) transcription activator protein PspF for negative regulation
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK
    J Mol Biol 394:764-75. 2009
    ....
  18. doi Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology
    Nicolas Joly
    Division of Biology, Imperial College London, South Kensington, London, UK
    FEMS Microbiol Rev 34:797-827. 2010
    ....
  19. pmc A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase
    Patricia C Burrows
    Division of Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 107:9376-81. 2010
    ..Significantly, this work highlights that prehydrolysis states of ATPases are functionally important in the molecular transformations they drive...
  20. doi Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor
    Sivaramesh Wigneshweraraj
    Department of Microbiology, Division of Investigative Sciences, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
    Mol Microbiol 68:538-46. 2008
    ..Here, we summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery...
  21. doi Subunit dynamics and nucleotide-dependent asymmetry of an AAA(+) transcription complex
    Nan Zhang
    Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, UK Electronic address
    J Mol Biol 426:71-83. 2014
    ..Outcomes reconcile low- and high-resolution structures and yield a partial sequential ATP hydrolysis model for bEBPs. ..
  22. pmc Single chain forms of the enhancer binding protein PspF provide insights into geometric requirements for gene activation
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
    J Biol Chem 286:12734-42. 2011
    ..We now propose that the hexamer functions with asymmetric organization, potentially involving a split planar (open ring) or spiral character...
  23. pmc Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
    Baojun Wang
    Centre for Synthetic Biology and Innovation and Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
    Nat Commun 2:508. 2011
    ..The results show that new genetic logic devices can be engineered predictably from novel native orthogonal biological control elements using quantitatively in-context characterized parts...
  24. ncbi Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation
    Jorg Schumacher
    Division of Biology, Imperial College London, London, SW7 2AZ, UK
    J Struct Biol 156:190-9. 2006
    ..Parallels with the substrate binding elements near the central pore of other AAA+ members are drawn. We propose a structural model of EBPs in complex with a sigma(54)-RNAP-promoter complex...