Gabriel Waksman

Summary

Affiliation: University of London
Country: UK

Publications

  1. ncbi request reprint The role of water in computational and experimental derivation of binding thermodynamics in SH2 domains
    Sebastien Geroult
    Institute of Structural Molecular Biology at UCL and Birkbek, Malet Street, London WC1 7HX, UK
    Chem Biol Drug Des 67:38-45. 2006
  2. pmc Structure of the outer membrane complex of a type IV secretion system
    Vidya Chandran
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
    Nature 462:1011-5. 2009
  3. pmc Architectures and biogenesis of non-flagellar protein appendages in Gram-negative bacteria
    Remi Fronzes
    School of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College University College London, London, UK
    EMBO J 27:2271-80. 2008
  4. pmc Repetitive architecture of the Haemophilus influenzae Hia trimeric autotransporter
    Guoyu Meng
    Institute of Structural and Molecular Biology at UCL Birkbeck, London, UK
    J Mol Biol 384:824-36. 2008
  5. ncbi request reprint SH2 domains: role, structure and implications for molecular medicine
    Gabriel Waksman
    Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, Saint Louis, MO 63110, USA
    Expert Rev Mol Med 6:1-18. 2004
  6. doi request reprint Structural determinants of polymerization reactivity of the P pilus adaptor subunit PapF
    Denis Verger
    Institute of Structural and Molecular Biology, University College London, Birkbeck College, Malet Street, London WC1E 7HX, UK
    Structure 16:1724-31. 2008
  7. pmc NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system
    Richard Bayliss
    Institute of Structural Molecular Biology, University College London Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
    Proc Natl Acad Sci U S A 104:1673-8. 2007
  8. pmc Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system
    Karin Wallden
    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, London WC1E 7HX, United Kingdom
    Proc Natl Acad Sci U S A 109:11348-53. 2012
  9. pmc Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria
    Jerome S Pinkner
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:17897-902. 2006
  10. pmc Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase
    Stephen Hare
    School of Crystallography, Birkbeck College, London, UK
    EMBO J 26:4926-34. 2007

Research Grants

  1. Structure of Proteins Involved in Bacterial Pathogenesis
    Gabriel Waksman; Fiscal Year: 2001
  2. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 1999
  3. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2000
  4. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2002
  5. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2001
  6. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2003
  7. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2002
  8. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2001
  9. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2000
  10. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2003

Collaborators

Detail Information

Publications70

  1. ncbi request reprint The role of water in computational and experimental derivation of binding thermodynamics in SH2 domains
    Sebastien Geroult
    Institute of Structural Molecular Biology at UCL and Birkbek, Malet Street, London WC1 7HX, UK
    Chem Biol Drug Des 67:38-45. 2006
    ..This prompted us to experimentally determine the heat capacity change for each of the peptides and we found them to coincide with the values of the peaks. The implications of such findings are discussed...
  2. pmc Structure of the outer membrane complex of a type IV secretion system
    Vidya Chandran
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
    Nature 462:1011-5. 2009
    ..Comparison of the cryo-electron microscopy (cryo-EM) and crystallographic structures points to conformational changes regulating channel opening and closing...
  3. pmc Architectures and biogenesis of non-flagellar protein appendages in Gram-negative bacteria
    Remi Fronzes
    School of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College University College London, London, UK
    EMBO J 27:2271-80. 2008
    ..Here, we review the five known classes of Gram-negative non-flagellar appendages from a biosynthetic and structural point of view...
  4. pmc Repetitive architecture of the Haemophilus influenzae Hia trimeric autotransporter
    Guoyu Meng
    Institute of Structural and Molecular Biology at UCL Birkbeck, London, UK
    J Mol Biol 384:824-36. 2008
    ..Overall, this study provides important insights into the mechanism of Hia adhesive activity and the overall structure of trimeric autotransporters...
  5. ncbi request reprint SH2 domains: role, structure and implications for molecular medicine
    Gabriel Waksman
    Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, Saint Louis, MO 63110, USA
    Expert Rev Mol Med 6:1-18. 2004
    ....
  6. doi request reprint Structural determinants of polymerization reactivity of the P pilus adaptor subunit PapF
    Denis Verger
    Institute of Structural and Molecular Biology, University College London, Birkbeck College, Malet Street, London WC1E 7HX, UK
    Structure 16:1724-31. 2008
    ..Using electrospray-ionization mass spectrometry, we show that mutations in the P5 region result in increased DSE rates. Thus, partial obstruction of the P5 pocket serves as a modulating mechanism of DSE...
  7. pmc NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system
    Richard Bayliss
    Institute of Structural Molecular Biology, University College London Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
    Proc Natl Acad Sci U S A 104:1673-8. 2007
    ..tumefaciens inserts in the membrane and protrudes extracellularly. This complex structure elucidates the molecular basis for the interaction between two essential components of a T4S system...
  8. pmc Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system
    Karin Wallden
    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, London WC1E 7HX, United Kingdom
    Proc Natl Acad Sci U S A 109:11348-53. 2012
    ..Remarkably, VirB4 is observed bound to the side of the complex where it is ideally placed to play its known regulatory role in substrate transfer...
  9. pmc Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria
    Jerome S Pinkner
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:17897-902. 2006
    ..These pilicides thus target key virulence factors in pathogenic bacteria and represent a promising proof of concept for developing drugs that function by targeting virulence factors...
  10. pmc Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase
    Stephen Hare
    School of Crystallography, Birkbeck College, London, UK
    EMBO J 26:4926-34. 2007
    ..From the structure, it is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion, a suggestion confirmed by results of in vitro ATPase assay and in vivo pull-down experiments...
  11. pmc The tandem Src homology 2 domain of the Syk kinase: a molecular device that adapts to interphosphotyrosine distances
    Sangaralingam Kumaran
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 100:14828-33. 2003
    ....
  12. pmc Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter
    Guoyu Meng
    Institute of Structural Molecular Biology at UCL Birkbeck, London, UK
    EMBO J 25:2297-304. 2006
    ..Overall, this study provides important insights into the mechanism of translocation in trimeric autotransporters...
  13. ncbi request reprint A large domain swap in the VirB11 ATPase of Brucella suis leaves the hexameric assembly intact
    Stephen Hare
    School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK
    J Mol Biol 360:56-66. 2006
    ..However, the monomer differs dramatically from that of Hp0525 by a large domain swap that leaves the hexameric assembly intact but profoundly alters the nucleotide-binding site and the interface between subunits...
  14. pmc Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding
    Haifeng Jia
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
    J Mol Biol 411:633-48. 2011
    ..Binding of UvrD to DNA and ATP binding and hydrolysis also affect the rotational conformational state of the 2B sub-domain, suggesting that 2B sub-domain rotation is coupled to the function of this nucleic acid motor enzyme...
  15. pmc Crystal structure of the P pilus rod subunit PapA
    Denis Verger
    Institute of Structural Molecular Biology, University College London and Birkbeck College, London, United Kingdom
    PLoS Pathog 3:e73. 2007
    ....
  16. doi request reprint Structure of a type IV secretion system core complex
    Remi Fronzes
    Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London, WC1E 7HX, UK
    Science 323:266-8. 2009
    ..Overall, the T4SS core complex structure is different in both architecture and composition from the other known double membrane-spanning secretion system that has been structurally characterized...
  17. ncbi request reprint Two-step and one-step secretion mechanisms in Gram-negative bacteria: contrasting the type IV secretion system and the chaperone-usher pathway of pilus biogenesis
    Ana Toste Rêgo
    Institute of Structural and Molecular Biology, Birkbeck and University College London, Malet Street, London, WC1E 7HX, UK
    Biochem J 425:475-88. 2010
    ..The present review provides an example for each of these two classes of secretion systems and contrasts the various solutions evolved to secrete substrates...
  18. pmc Structures of two core subunits of the bacterial type IV secretion system, VirB8 from Brucella suis and ComB10 from Helicobacter pylori
    Laurent Terradot
    Institute of Structural Molecular Biology, Malet Street, London WC1E 7HX, UK
    Proc Natl Acad Sci U S A 102:4596-601. 2005
    ....
  19. pmc Structural basis for host recognition by the Haemophilus influenzae Hia autotransporter
    Hye Jeong Yeo
    Institute of Structural Molecular Biology, Birkbeck and University College London, Malet Street, London, UK
    EMBO J 23:1245-56. 2004
    ..Hia is a novel example of a bacterial trimeric adhesin and may be the prototype member of a large family of bacterial virulence proteins with a similar architecture...
  20. ncbi request reprint Structural basis of tropism of Escherichia coli to the bladder during urinary tract infection
    Chia Suei Hung
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
    Mol Microbiol 44:903-15. 2002
    ..coli (EHEC) possess a sequence variation within the mannose-binding pocket of FimH, suggesting a naturally occurring mechanism of attenuation in EHEC bacteria that would prevent them from being targeted to the urinary tract...
  21. pmc Structural homology between the C-terminal domain of the PapC usher and its plug
    Bradley Ford
    Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    J Bacteriol 192:1824-31. 2010
    ..This structure paves the way for further functional analysis targeting surfaces common to both the plug and the C-terminal domain of PapC...
  22. pmc Molecular mechanism of P pilus termination in uropathogenic Escherichia coli
    Denis Verger
    Institute of Structural Molecular Biology, University College London, Birkbeck College, Malet Street, London WC1E 7HX, UK
    EMBO Rep 7:1228-32. 2006
    ....
  23. ncbi request reprint Structural and thermodynamic basis for the interaction of the Src SH2 domain with the activated form of the PDGF beta-receptor
    Olga Y Lubman
    Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
    J Mol Biol 328:655-68. 2003
    ..Surprisingly, we show that water plays a role in the recognition process...
  24. pmc Molecular basis of usher pore gating in Escherichia coli pilus biogenesis
    Ender Volkan
    Department of Molecular Microbiology and Center for Women s Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO 63110
    Proc Natl Acad Sci U S A 110:20741-6. 2013
    ..These studies provide insights into the molecular basis of usher pore gating and its roles in pilus biogenesis and OM permeability. ..
  25. pmc Fiber formation across the bacterial outer membrane by the chaperone/usher pathway
    Han Remaut
    Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London, WC1E 7HX, United Kingdom
    Cell 133:640-52. 2008
    ..These structures capture the secretion of a virulence factor across the outer membrane of gram-negative bacteria...
  26. pmc Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine
    Ender Volkan
    Department of Molecular Microbiology, Center for Women s Infectious Diseases Research, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 109:9563-8. 2012
    ..Overall, our studies reveal the cooperative, active roles played by periplasmic domains of the usher to initiate, grow, and terminate a prototypical chaperone-usher pathway pilus...
  27. pmc Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate
    Gilles Phan
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
    Nature 474:49-53. 2011
    ..The FimD-FimC-FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate...
  28. ncbi request reprint Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases
    Paul J Rothwell
    Institute of Structural Molecular Biology, Birkbeck College and University College London, Malet Street, London WC1E 7HX, United Kingdom
    Mol Cell 19:345-55. 2005
    ..We propose that the rate-limiting step occurs after the closing of the fingers subdomain and is caused by local reorganization events in the active site...
  29. doi request reprint Semisynthetic Src SH2 domains demonstrate altered phosphopeptide specificity induced by incorporation of unnatural lysine derivatives
    Satpal Virdee
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London, UK, WC1E 7HX
    Chem Biol 17:274-84. 2010
    ....
  30. ncbi request reprint The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket
    Agustin O Pineda
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    J Biol Chem 279:39824-8. 2004
    ....
  31. pmc Structural and energetic basis of folded-protein transport by the FimD usher
    Sebastian Geibel
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
    Nature 496:243-6. 2013
    ..We show that the circular binding interface between the pore lumen and the folded substrate participates in transport by defining a low-energy pathway along which the nascent pilus polymer is guided during secretion...
  32. doi request reprint Crystal structure of a vFlip-IKKgamma complex: insights into viral activation of the IKK signalosome
    Claire Bagneris
    Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK
    Mol Cell 30:620-31. 2008
    ..In addition to identifying and subsequently probing the ks-vFLIP-IKKgamma interface, we have also investigated the effects of a mutation implicated in the genetic disorder anhydrotic ectodermal dysplasia with immunodeficiency (EDA-ID)...
  33. pmc Unveiling molecular scaffolds of the type IV secretion system
    Hye Jeong Yeo
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    J Bacteriol 186:1919-26. 2004
  34. ncbi request reprint Donor-strand exchange in chaperone-assisted pilus assembly proceeds through a concerted beta strand displacement mechanism
    Han Remaut
    Institute of Structural Molecular Biology at UCL Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
    Mol Cell 22:831-42. 2006
    ..The data also suggest a capping reaction displacing DSE toward product formation. These results support a zip-in-zip-out mechanism for DSE and a catalytic role for the usher, the molecular platform at which pili are assembled...
  35. pmc Structure of a bacterial type IV secretion core complex at subnanometre resolution
    Angel Rivera-Calzada
    Department of Biological Sciences, Institute of Structural and Molecular Biology, UCL and Birkbeck, London WC1E 7HX, UK
    EMBO J 32:1195-204. 2013
    ..Our results provide new structural insights on the CC, from which the essential features of T4S system mechanisms can be derived...
  36. pmc Dissection of pilus tip assembly by the FimD usher monomer
    William J Allen
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
    J Mol Biol 425:958-67. 2013
    ..Furthermore, by establishing the kinetics of usher-catalysed reactions between various pilus subunits, we establish a complete kinetic model of tip fibrillum assembly, able to account for the order of subunits in native type 1 pili...
  37. pmc Structural biology of the chaperone-usher pathway of pilus biogenesis
    Gabriel Waksman
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London, UK
    Nat Rev Microbiol 7:765-74. 2009
    ..Other studies have provided the molecular basis of host recognition by CU pili. The knowledge that has been gathered about both the assembly of and host recognition by CU pili has been harnessed to design promising antibiotic compounds...
  38. ncbi request reprint Resonance assignments of the complex between TraN and the C-terminal domain of TraO from the conjugative plasmid pKM101
    Richard Harris
    Institute of Structural Molecular Biology, UCL Birkbeck, Malet Street, WC1E 7HX, London, UK
    J Biomol NMR 36:31. 2006
  39. pmc The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA
    Savvas N Savvides
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
    Protein Sci 13:1942-7. 2004
    ..The structure also reveals the conservation of molecular contacts between successive tetramers mediated by the L(45) loops as seen in two other crystal forms of SSBc, suggesting a possible functional relevance of this interaction...
  40. ncbi request reprint Molecular recognition by SH2 domains
    J Michael Bradshaw
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Adv Protein Chem 61:161-210. 2002
    ..Hence, the future should bring further investigations of the mechanisms by which SH2 domain ligation alters the enzymatic activity and cellular localization of SH2 domain-containing proteins...
  41. pmc The 2B domain of the Escherichia coli Rep protein is not required for DNA helicase activity
    Wei Cheng
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 99:16006-11. 2002
    ..These studies show that the 2B domain of Rep is not required for DNA helicase activity in vivo or in vitro, and that it does not facilitate DNA unwinding in vitro...
  42. pmc Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101
    Hye Jeong Yeo
    Institute of Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
    Proc Natl Acad Sci U S A 100:15947-52. 2003
    ..Structure-based site-directed mutagenesis followed by functional studies indicates that VirB5 proteins participate in protein-protein interactions important for pilus assembly and function...
  43. pmc The crystal structure of a partial mouse Notch-1 ankyrin domain: repeats 4 through 7 preserve an ankyrin fold
    Olga Y Lubman
    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Protein Sci 14:1274-81. 2005
    ..The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation...
  44. pmc VirB11 ATPases are dynamic hexameric assemblies: new insights into bacterial type IV secretion
    Savvas N Savvides
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO 63110, USA
    EMBO J 22:1969-80. 2003
    ..Biochemical characterization of mutant forms of HP0525 coupled with electron microscopy and in vivo assays support such hypothesis, and establish the relevance of VirB11s ATPases as drug targets against pathogenic bacteria...
  45. pmc Structural insights into the membrane-extracted dimeric form of the ATPase TraB from the Escherichia coli pKM101 conjugation system
    Eric Durand
    Institute of Structural and Molecular Biology, UCL Birkbeck, Malet Street, London WC1E 7HX, UK
    BMC Struct Biol 11:4. 2011
    ..The X-ray crystal structures of VirB11 and VirD4 have already been solved but VirB4 has proven to be reluctant to any structural investigation so far...
  46. ncbi request reprint Pilus biogenesis at the outer membrane of Gram-negative bacterial pathogens
    William J Allen
    Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, WC1E 7HX London, UK
    Curr Opin Struct Biol 22:500-6. 2012
    ..Such knowledge will be particularly important in the future, as we approach an era of widespread resistance to common antibiotics and require new targets...
  47. ncbi request reprint Structure and mechanism of DNA polymerases
    Paul J Rothwell
    Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
    Adv Protein Chem 71:401-40. 2005
    ..In this review, we present and discuss the kinetic, structural, and single-molecule works that have contributed to our understanding of DNA polymerase function...
  48. ncbi request reprint Protein oligomerization in the bacterial outer membrane (Review)
    Guoyu Meng
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK
    Mol Membr Biol 26:136-45. 2009
    ..Here we review the current understanding of oligomerization in the bacterial outer membrane from a structural and functional point of view...
  49. doi request reprint Structural analysis of the Saf pilus by electron microscopy and image processing
    Osman Salih
    Institute of Structural Molecular Biology at UCL Birkbeck, London WC1E 7HX, UK
    J Mol Biol 379:174-87. 2008
    ..Short intersubunit linker regions provide the molecular basis for flexibility of the Saf pilus by acting as molecular hinges allowing a large range of movement between consecutive subunits in the fibre...
  50. pmc The structural biology of type IV secretion systems
    Remi Fronzes
    Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, UK
    Nat Rev Microbiol 7:703-14. 2009
    ..This Review focuses on the structural advances that have been made over the past 10 years and how the corresponding structural insights have helped to elucidate many of the details of the mechanism of type IV secretion...
  51. ncbi request reprint Protein-protein interaction through beta-strand addition
    Han Remaut
    Institute of Structural Molecular Biology, School of Crystallography, Birkbeck College, University College London, London, WC1E 7HX, UK
    Trends Biochem Sci 31:436-44. 2006
    ..A survey of protein-protein complexes in the protein data bank identifies beta-strand additions in many important metabolic pathways. Targeting these interactions might, thus, provide novel routes for rational drug design...
  52. pmc Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems
    Adam Redzej
    Institute of Structural and Molecular Biology, UCL and Birkbeck, Malet Street, London, WC1E 7HX, UK
    Mol Microbiol 89:324-33. 2013
    ..Overall, this study provides the first evidence that translocation signals can be part of larger structural scaffolds, overlapping with translocation-independent activities. ..
  53. doi request reprint Crystal structure of the MrkD1P receptor binding domain of Klebsiella pneumoniae and identification of the human collagen V binding interface
    Ana Toste Rêgo
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London, WC1E 7HX, UK
    Mol Microbiol 86:882-93. 2012
    ....
  54. doi request reprint Structural biology of periplasmic chaperones
    William J Allen
    Institute of Structural and Molecular Biology, Birkbeck and University College London, London WC1E 7HX, UK
    Adv Protein Chem Struct Biol 78:51-97. 2009
    ..This chapter aims to provide an overview of protein chaperones so far identified in the periplasm and how structural biology has assisted with the elucidation of their functions...
  55. ncbi request reprint A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1
    Paul J Rothwell
    Institute of Structural Molecular Biology, Birkbeck College and University College London, Malet Street, London, WC1E 7HX, United Kingdom
    J Biol Chem 282:28884-92. 2007
    ..As the only difference between the (E x p/t) complexes is the templating base, it would suggest an important role for the templating base in initial ground state selection...
  56. ncbi request reprint Structural biology of bacterial pathogenesis
    Han Remaut
    Institute of Structural Molecular Biology, School of Crystallography, Birkbeck College, London, UK
    Curr Opin Struct Biol 14:161-70. 2004
    ..Finally, the structures of complexes of secreted virulence factors bound to their host targets have unravelled the mechanisms by which bacterial pathogens exploit cellular processes to their advantage...
  57. doi request reprint Molecular architecture of bacterial type IV secretion systems
    Gabriel Waksman
    Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
    Trends Biochem Sci 35:691-8. 2010
    ..Recent structural data, namely the electron microscopy structure of the T4S core complex and the atomic-resolution structure of its outer-membrane pore, have profoundly altered our understanding of T4S architecture and mechanisms...
  58. doi request reprint Crystallography and electron microscopy of chaperone/usher pilus systems
    Sebastian Geibel
    Institute of Structural Molecular Biology, Birkbeck and University College London, London, UK
    Adv Exp Med Biol 715:159-74. 2011
    ..Here we review the structural biology of the chaperone-usher pathway that has helped to understand the mechanisms by which biogenesis of an important class of bacterial organelles occurs...
  59. pmc Chaperone-usher pathways: diversity and pilus assembly mechanism
    Andreas Busch
    Institute of Structural and Molecular Biology, University College London, Malet Street, WC1E 7HX London, UK
    Philos Trans R Soc Lond B Biol Sci 367:1112-22. 2012
    ....
  60. pmc Structure of a type IV secretion system
    Harry H Low
    1 Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK 2 3
    Nature 508:550-3. 2014
    ..Our results show a secretion system with markedly different architecture, and consequently mechanism, to other known bacterial secretion systems. ..
  61. ncbi request reprint Biochemical characterization of protein complexes from the Helicobacter pylori protein interaction map: strategies for complex formation and evidence for novel interactions within type IV secretion systems
    Laurent Terradot
    Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 South Euclid Avenue, Campus Box 8231, St Louis, MO 63110, USA
    Mol Cell Proteomics 3:809-19. 2004
    ..Finally, a third interaction was biochemically confirmed between CagA, a virulence factor secreted by the type IV secretion system encoded by the Cag pathogenicity island, and a non-type IV secretion protein, HP0496...
  62. ncbi request reprint Crystal structure of the anticoagulant slow form of thrombin
    Agustin O Pineda
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA
    J Biol Chem 277:40177-80. 2002
    ..The structure of the slow form explains the reduced specificity toward synthetic and natural substrates and suggests a molecular basis for its anticoagulant properties...
  63. ncbi request reprint Dissection of the energetic coupling across the Src SH2 domain-tyrosyl phosphopeptide interface
    Olga Y Lubman
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Ave, Saint Louis, MO 63110, USA
    J Mol Biol 316:291-304. 2002
    ..Thus, unexpectedly, mutations in the +1 binding region affect binding of other regions of the peptide. Such additional contacts may account for the high affinity interaction of the triple mutant for the pYEEI-containing peptide...
  64. ncbi request reprint Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations
    Sebastien Geroult
    Institute of Structural Molecular Biology, UCL and Birkbeck, Malet Street, WC1E 7HX London, United Kingdom
    Chem Biol Drug Des 70:87-99. 2007
    ..This study is the first to examine the dynamics of the water structure around the SH2 domain binding interface and contributes to our understanding of binding thermodynamics in SH2 domains...
  65. ncbi request reprint Structure and specificity of the SH2 domain
    Gabriel Waksman
    Institute of Structural Molecular Biology, University College London and Birkbeck College, Malet Street, London, WC1E 7HX, United Kingdom
    Cell 116:S45-8, 3 p following S48. 2004
  66. pmc Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry
    Rebecca J Rose
    Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
    Proc Natl Acad Sci U S A 105:12873-8. 2008
    ..The results reveal insights into the molecular mechanism by which subunit ordering during the assembly of this complex is achieved...
  67. pmc Dimerization and interactions of Brucella suis VirB8 with VirB4 and VirB10 are required for its biological activity
    Athanasios Paschos
    Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
    Proc Natl Acad Sci U S A 103:7252-7. 2006
    ..Changes at Y105, T201, R230, and at several other residues impaired the in vivo function of VirB8, suggesting that we have identified interaction sites of relevance in the natural biological context...
  68. ncbi request reprint Fiber assembly by the chaperone-usher pathway
    Frederic G Sauer
    Section of Microbial Pathogenesis, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Ave, New Haven, CT 06536, USA
    Biochim Biophys Acta 1694:259-67. 2004
    ..Chaperone dissociation releases the folding energy that drives subunit incorporation into the fiber, which grows through a pore formed by the outer-membrane usher...
  69. ncbi request reprint Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding
    James P Davidson
    Department of Chemistry and Biochemistry and The Institute of Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
    J Am Chem Soc 124:205-15. 2002
    ....
  70. ncbi request reprint Donor-strand exchange in chaperone-assisted pilus assembly revealed in atomic detail by molecular dynamics
    Rebecca J Rose
    Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
    J Mol Biol 375:908-19. 2008
    ..Together, the study provides an in-depth picture of DSE, including the first atomistic insights into the molecular events occurring during the zip-in-zip-out mechanism...

Research Grants13

  1. Structure of Proteins Involved in Bacterial Pathogenesis
    Gabriel Waksman; Fiscal Year: 2001
    ..abstract_text> ..
  2. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 1999
    ..Recently, sizable crystals of a DNA/SSBc complex have been grown. ..
  3. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2000
    ..Such structures will provide information on the mechanism of active unwinding by DNA-helicases and of passive unwinding by helix-destabilizing SSB proteins. ..
  4. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2002
    ..abstract_text> ..
  5. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2001
    ..Such structures will provide information on the mechanism of active unwinding by DNA-helicases and of passive unwinding by helix-destabilizing SSB proteins. ..
  6. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2003
    ..abstract_text> ..
  7. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2002
    ..Such structures will provide information on the mechanism of active unwinding by DNA-helicases and of passive unwinding by helix-destabilizing SSB proteins. ..
  8. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2001
    ..abstract_text> ..
  9. BIOPHYSICAL STUDIES OF SRC HOMOLOGY 2 DOMAINS
    Gabriel Waksman; Fiscal Year: 2000
    ..abstract_text> ..
  10. STRUCTURAL STUDIES OF DNA REPLICATION AND REPAIR
    Gabriel Waksman; Fiscal Year: 2003
    ..Such structures will provide information on the mechanism of active unwinding by DNA-helicases and of passive unwinding by helix-destabilizing SSB proteins. ..