AXEL BRUNGER

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion
    Marija Vrljic
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA
    Nat Struct Mol Biol 17:325-31. 2010
  2. pmc The longin SNARE VAMP7/TI-VAMP adopts a closed conformation
    Sandro Vivona
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA
    J Biol Chem 285:17965-73. 2010
  3. pmc Native α-synuclein induces clustering of synaptic-vesicle mimics via binding to phospholipids and synaptobrevin-2/VAMP2
    Jiajie Diao
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States Department of Structural Biology, Stanford University, Stanford, United States Departments of Photon Sciences, and Neurology and Neurological Sciences, Stanford University, Stanford, United States Howard Hughes Medical Institute, Stanford University, Stanford, United States
    elife 2:e00592. 2013
  4. pmc Disassembly of all SNARE complexes by N-ethylmaleimide-sensitive factor (NSF) is initiated by a conserved 1:1 interaction between α-soluble NSF attachment protein (SNAP) and SNARE complex
    Sandro Vivona
    Department of Molecular and Cellular Physiology, Stanford University Medical School, Stanford, California 94305, USA
    J Biol Chem 288:24984-91. 2013
  5. pmc Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex
    Ucheor B Choi
    Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
    Nat Struct Mol Biol 17:318-24. 2010
  6. pmc A smooth and differentiable bulk-solvent model for macromolecular diffraction
    T D Fenn
    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford, California, USA
    Acta Crystallogr D Biol Crystallogr 66:1024-31. 2010
  7. pmc Post-translational modifications and lipid binding profile of insect cell-expressed full-length mammalian synaptotagmin 1
    Marija Vrljic
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305 5432, USA
    Biochemistry 50:9998-10012. 2011
  8. pmc Synaptic proteins promote calcium-triggered fast transition from point contact to full fusion
    Jiajie Diao
    Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, Photon Science and Howard Hughes Medical Institute, Stanford University, Stanford, USA
    elife 1:e00109. 2012
  9. pmc Improving the accuracy of macromolecular structure refinement at 7 Å resolution
    Axel T Brunger
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Structure 20:957-66. 2012
  10. pmc Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
    Axel T Brunger
    Department of Molecular and Cellular Physiology, Stanford University, USA
    Acta Crystallogr D Biol Crystallogr 68:391-403. 2012

Collaborators

Detail Information

Publications68

  1. pmc Molecular mechanism of the synaptotagmin-SNARE interaction in Ca2+-triggered vesicle fusion
    Marija Vrljic
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA
    Nat Struct Mol Biol 17:325-31. 2010
    ..The loops resemble the membrane-interacting loops of certain viral fusion proteins in the postfusion state, suggesting unexpected similarities between both fusion systems...
  2. pmc The longin SNARE VAMP7/TI-VAMP adopts a closed conformation
    Sandro Vivona
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA
    J Biol Chem 285:17965-73. 2010
    ..This may indicate different regulatory mechanisms for SNARE complexes containing syntaxins and longins, respectively...
  3. pmc Native α-synuclein induces clustering of synaptic-vesicle mimics via binding to phospholipids and synaptobrevin-2/VAMP2
    Jiajie Diao
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States Department of Structural Biology, Stanford University, Stanford, United States Departments of Photon Sciences, and Neurology and Neurological Sciences, Stanford University, Stanford, United States Howard Hughes Medical Institute, Stanford University, Stanford, United States
    elife 2:e00592. 2013
    ..Synuclein may therefore lead to accumulation of synaptic vesicles at the active zone, providing a 'buffer' of synaptic vesicles, without affecting neurotransmitter release itself. DOI:http://dx.doi.org/10.7554/eLife.00592.001...
  4. pmc Disassembly of all SNARE complexes by N-ethylmaleimide-sensitive factor (NSF) is initiated by a conserved 1:1 interaction between α-soluble NSF attachment protein (SNAP) and SNARE complex
    Sandro Vivona
    Department of Molecular and Cellular Physiology, Stanford University Medical School, Stanford, California 94305, USA
    J Biol Chem 288:24984-91. 2013
    ..Subsequent additional α-SNAP binding events may occur as part of a processive disassembly mechanism. ..
  5. pmc Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex
    Ucheor B Choi
    Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
    Nat Struct Mol Biol 17:318-24. 2010
    ..The loop arrangement is similar to that of the crystal structure of SNARE-induced Ca(2+)-bound Syt3, suggesting a common mechanism by which the interaction between synaptotagmins and SNAREs aids in Ca(2+)-triggered fusion...
  6. pmc A smooth and differentiable bulk-solvent model for macromolecular diffraction
    T D Fenn
    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford, California, USA
    Acta Crystallogr D Biol Crystallogr 66:1024-31. 2010
    ..The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography...
  7. pmc Post-translational modifications and lipid binding profile of insect cell-expressed full-length mammalian synaptotagmin 1
    Marija Vrljic
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305 5432, USA
    Biochemistry 50:9998-10012. 2011
    ..These results suggest a conserved lipid binding mechanism in which Ca(2+)-independent interactions are mediated via a lysine rich region of the C2B domain while Ca(2+)-dependent interactions are mediated via the Ca(2+)-binding loops...
  8. pmc Synaptic proteins promote calcium-triggered fast transition from point contact to full fusion
    Jiajie Diao
    Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, Photon Science and Howard Hughes Medical Institute, Stanford University, Stanford, USA
    elife 1:e00109. 2012
    ..Synaptic proteins may have evolved to select this immediate pathway out of a heterogeneous network of possible membrane fusion pathways.DOI:http://dx.doi.org/10.7554/eLife.00109.001...
  9. pmc Improving the accuracy of macromolecular structure refinement at 7 Å resolution
    Axel T Brunger
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Structure 20:957-66. 2012
    ..We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution...
  10. pmc Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum
    Axel T Brunger
    Department of Molecular and Cellular Physiology, Stanford University, USA
    Acta Crystallogr D Biol Crystallogr 68:391-403. 2012
    ..This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence...
  11. pmc X-ray structure determination at low resolution
    Axel T Brunger
    Howard Hughes Medical Institute, Stanford University, USA
    Acta Crystallogr D Biol Crystallogr 65:128-33. 2009
    ..It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible...
  12. pmc Receptor and substrate interactions of clostridial neurotoxins
    Axel T Brunger
    The Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science, Stanford University, J H Clark Center, E300C, 318 Campus Drive, Stanford, CA 94305, USA
    Toxicon 54:550-60. 2009
    ..After its translocation the enzymatically active light chain specifically hydrolyses specific SNARE proteins, preventing SNARE complex assembly and thereby blocking exocytosis of neurotransmitter...
  13. ncbi request reprint Highly specific interactions between botulinum neurotoxins and synaptic vesicle proteins
    A T Brunger
    Howard Hughes Medical Institute, Stanford, CA, USA
    Cell Mol Life Sci 65:2296-306. 2008
    ..In this review we discuss the structural basis for botulinum toxin's exquisite specificity for its neuronal cell-surface receptors and intracellular SNARE targets...
  14. pmc Botulinum neurotoxin heavy chain belt as an intramolecular chaperone for the light chain
    Axel T Brunger
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA
    PLoS Pathog 3:1191-4. 2007
  15. ncbi request reprint NSF and p97/VCP: similar at first, different at last
    Axel T Brunger
    Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, and Stanford Synchrotron Radiation Laboratory, Stanford University, James H Clark Center E300 C, 318 Campus Drive, Stanford, CA 94305 5432, USA
    FEBS Lett 555:126-33. 2003
    ..These functional differences are now corroborated by major structural differences based on recent crystallographic and cryo-electron microscopy studies. This review discusses these recent findings...
  16. pmc Three-dimensional molecular modeling with single molecule FRET
    Axel T Brunger
    The Howard Hughes Medical Institute, Stanford University, CA 94305, USA
    J Struct Biol 173:497-505. 2011
    ....
  17. pmc Single-molecule studies of the neuronal SNARE fusion machinery
    Axel T Brunger
    The Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science, Stanford University, CA 94305, USA
    Annu Rev Biochem 78:903-28. 2009
    ..Some of the findings are provocative, such as the possibility of parallel and antiparallel SNARE complexes or of vesicle docking with only syntaxin and synaptobrevin, but have been confirmed by other experiments...
  18. ncbi request reprint Version 1.2 of the Crystallography and NMR system
    Axel T Brunger
    The Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, California 94305, USA
    Nat Protoc 2:2728-33. 2007
    ..Other advances include the ability to apply thermal factor sharpening to electron density maps. Consistent with the modular design of CNS, these additions and changes were implemented in the high-level computing language of CNS...
  19. ncbi request reprint High resolution structure, stability, and synaptotagmin binding of a truncated neuronal SNARE complex
    James A Ernst
    Howard Hughes Medical Institute, Stanford University, California 94305, USA
    J Biol Chem 278:8630-6. 2003
    ..The truncated SNARE complex is monomeric, and it retains binding to synaptotagmin I...
  20. ncbi request reprint 2.3 A crystal structure of tetanus neurotoxin light chain
    Mark A Breidenbach
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA
    Biochemistry 44:7450-7. 2005
    ....
  21. pmc Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
    Gunnar F Schröder
    Department of Structural Biology, Stanford University Stanford, CA 94305, USA
    Structure 15:1630-41. 2007
    ..Our algorithm is robust even for noise-added density maps and has a large radius of convergence for our test case. The DEN restraints can also be used to enhance reciprocal space simulated annealing refinement...
  22. ncbi request reprint Molecular dynamics applied to X-ray structure refinement
    Axel T Brunger
    The Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
    Acc Chem Res 35:404-12. 2002
    ..The theory and practice of the method are reviewed, and some recent improvements are described...
  23. doi request reprint Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change
    Jason M Davies
    Department of Structural Biology, Stanford University, Stanford, CA 94305 5432, USA
    Structure 16:715-26. 2008
    ....
  24. ncbi request reprint Structural basis of FFAT motif-mediated ER targeting
    Stephen E Kaiser
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Structure 13:1035-45. 2005
    ..Our data establish the structural basis of FFAT-mediated ER targeting and suggest that FFAT-targeted proteins play an important role in determining ER morphology...
  25. pmc Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion
    Peter M Kasson
    Medical Scientist Training and Biophysics Programs, Department of Computer Science, Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:11916-21. 2006
    ....
  26. pmc Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex
    Shuya Fukai
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, James H Clark Center, E300C, 318 Campus Drive, Stanford, CA 94305 5432, USA
    EMBO J 22:3267-78. 2003
    ..Comparison of the structures of GppNHp- and GDP-bound RalA suggests a nucleotide-dependent switch mechanism for Sec5 binding...
  27. pmc Polarizable atomic multipole X-ray refinement: application to peptide crystals
    Michael J Schnieders
    Department of Chemistry, Stanford University, Stanford, CA 94305, USA
    Acta Crystallogr D Biol Crystallogr 65:952-65. 2009
    ..For a series of four peptide crystals, the AMOEBA-IAS model lowered R(free) by 20-40% relative to the original spherically symmetric scattering model...
  28. ncbi request reprint Computational aspects of high-throughput crystallographic macromolecular structure determination
    Paul D Adams
    Lawrence Berkeley Laboratory, Berkeley, CA, USA
    Methods Biochem Anal 44:75-87. 2003
  29. ncbi request reprint Structures of neuroligin-1 and the neuroligin-1/neurexin-1 beta complex reveal specific protein-protein and protein-Ca2+ interactions
    Demet Arac
    Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
    Neuron 56:992-1003. 2007
    ..Our results provide molecular insights for understanding the role of cell-adhesion proteins in synapse function...
  30. pmc Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185
    Alondra Schweizer Burguete
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 132:286-98. 2008
    ....
  31. ncbi request reprint Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface
    Jun Aishima
    Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford, CA, USA
    Acta Crystallogr D Biol Crystallogr 61:1354-63. 2005
    ..Generalization of the method to recognition of common features across multiple contour levels could lead to powerful automatic fitting methods that perform well even at low resolution...
  32. ncbi request reprint The structure of the yeast plasma membrane SNARE complex reveals destabilizing water-filled cavities
    Pavel Strop
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA
    J Biol Chem 283:1113-9. 2008
    ..Mutagenesis experiments suggest that the water-filled cavities contribute to the lower stability of the S. cerevisiae complex...
  33. ncbi request reprint Structural and biochemical studies of botulinum neurotoxin serotype C1 light chain protease: implications for dual substrate specificity
    Rongsheng Jin
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305, USA
    Biochemistry 46:10685-93. 2007
    ..However, mutagenesis experiments show that the alpha-exosite of BoNT/C1 plays a less stringent role in substrate discrimination in comparison to that of BoNT/A, which could account for its dual substrate specificity...
  34. ncbi request reprint Botulinum neurotoxin B recognizes its protein receptor with high affinity and specificity
    Rongsheng Jin
    Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
    Nature 444:1092-5. 2006
    ..Our results provide the basis for the rational development of preventive vaccines or inhibitors against these neurotoxins...
  35. pmc Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations
    Keith Weninger
    The Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 4060, USA
    Proc Natl Acad Sci U S A 100:14800-5. 2003
    ....
  36. pmc Single molecule observation of liposome-bilayer fusion thermally induced by soluble N-ethyl maleimide sensitive-factor attachment protein receptors (SNAREs)
    Mark E Bowen
    The Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, California, USA
    Biophys J 87:3569-84. 2004
    ..Furthermore, although SNARE complexes involved in liposome docking preferentially assemble into a parallel configuration, both parallel and antiparallel configurations were observed...
  37. ncbi request reprint Nucleotide dependent motion and mechanism of action of p97/VCP
    Byron DeLaBarre
    Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, and Stanford Synchrotron Radiation Laboratory, Stanford University, J H Clark Center E300 C, 318 Campus Drive, Stanford, CA 94305 5432, USA
    J Mol Biol 347:437-52. 2005
    ....
  38. pmc Single-molecule studies of synaptotagmin and complexin binding to the SNARE complex
    Mark E Bowen
    The Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA
    Biophys J 89:690-702. 2005
    ..These results demonstrate that single molecule FRET can be used as a "spectroscopic ruler" to simultaneously gain structural and kinetic information about transient multiprotein complexes at the membrane interface...
  39. pmc Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase
    Rongsheng Jin
    Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 5432, USA
    EMBO J 24:2064-74. 2005
    ..Structural and biochemical data show that Exo84 and Sec5 competitively bind to active RalA. Taken together, these results further strengthen the proposed role of RalA-regulated assembly of the Sec6/8 complex...
  40. pmc Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A
    Jorge E Zuniga
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, United States of America
    PLoS ONE 5:e11378. 2010
    ..Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors...
  41. pmc Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules
    Timothy D Fenn
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA
    Biophys J 98:2984-92. 2010
    ..The polarizable atomic multipole electrostatics model implemented in the AMOEBA force field is applicable and informative for crystal structures solved at any resolution...
  42. pmc Quantitative imaging of lymphocyte membrane protein reorganization and signaling
    Peter M Kasson
    Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
    Biophys J 88:579-89. 2005
    ..Our methods can be generalized to a range of cell-signaling phenomena and enable novel applications not feasible with single-particle studies, such as analysis of subcellular protein localization in live organ culture...
  43. pmc A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate
    Jorge E Zuniga
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Structure 16:1588-97. 2008
    ..Our inhibitor is specific for BoNT/A as it does not inhibit other BoNT serotypes or thermolysin...
  44. ncbi request reprint Structure and function of SNARE and SNARE-interacting proteins
    Axel T Brunger
    Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Q Rev Biophys 38:1-47. 2005
    ..However, significantly more work will be required to reconstitute an in vitro system that faithfully mimics the Ca2+-triggered fusion of a synaptic vesicle at the active zone...
  45. ncbi request reprint Structural and functional comparisons of nucleotide pyrophosphatase/phosphodiesterase and alkaline phosphatase: implications for mechanism and evolution
    Jesse G Zalatan
    Department of Chemistry, Stanford University, Stanford, California 94305 5307, USA
    Biochemistry 45:9788-803. 2006
    ....
  46. pmc Transglutaminase 2 undergoes a large conformational change upon activation
    Daniel M Pinkas
    Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
    PLoS Biol 5:e327. 2007
    ....
  47. pmc Ab initio molecular-replacement phasing for symmetric helical membrane proteins
    Pavel Strop
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, and Stanford Synchrotron Radiation Laboratory, Stanford University, James H Clark Center E300, Stanford, California 94305, USA
    Acta Crystallogr D Biol Crystallogr 63:188-96. 2007
    ..The method does not require high-resolution diffraction data and can be used to obtain phases for symmetrical helical membrane proteins with one or two helices per monomer...
  48. ncbi request reprint Structure of a human A-type potassium channel interacting protein DPPX, a member of the dipeptidyl aminopeptidase family
    Pavel Strop
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford University, James H Clark Center E300, 318 Campus Drive, Stanford, CA 94305, USA
    J Mol Biol 343:1055-65. 2004
    ..However, the arrangement of residues is inconsistent with that of canonical serine proteases and DPPX is unlikely to function as a protease (dipeptidyl aminopeptidase)...
  49. ncbi request reprint Mutational analysis of synaptobrevin transmembrane domain oligomerization
    Mark E Bowen
    The Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305 5489, USA
    Biochemistry 41:15861-6. 2002
    ..We estimate a dissociation constant of 10 mM for synaptobrevin dimerization in detergent. Thus, the dimerization of synaptobrevin in membranes is very weak, questioning any possible functional role for this association in vivo...
  50. pmc Neurexins physically and functionally interact with GABA(A) receptors
    Chen Zhang
    Department of Molecular and Cellular Physiology, Stanford University, 1050 Arastradero Road, Palo Alto, CA 94304 5543, USA
    Neuron 66:403-16. 2010
    ..Our findings suggest that besides their other well-documented interactions, presynaptic neurexins directly act on postsynaptic GABA(A) receptors, which may contribute to regulate the excitatory/inhibitory balance in brain...
  51. pmc Neuroligin-1 performs neurexin-dependent and neurexin-independent functions in synapse validation
    Jaewon Ko
    Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Palo Alto, CA 94304 5543, USA
    EMBO J 28:3244-55. 2009
    ..Thus, neuroligin-1 performs diverse synaptic functions by mechanisms that include as essential components of alpha-neurexin binding and neuroligin dimerization, but extend beyond these activities...
  52. ncbi request reprint Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains
    Byron DeLaBarre
    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, James H Clark Center E300 C, 318 Campus Drive, Stanford, California 94305 5432, USA
    Nat Struct Biol 10:856-63. 2003
    ..Structural and functional data imply a communication mechanism between the AAA domains. A Zn(2+) occludes the central pore of the hexamer, suggesting that substrate does not thread through the pore of the molecule...
  53. pmc Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p
    Daqi Tu
    Department of Molecular and Cellular Physiology, Stanford University and Howard Hughes Medical Institute, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 104:15599-606. 2007
    ..Thus, Ufd2p can function as a bona fide E3 ubiquitin ligase to promote ubiquitin chain elongation on a substrate...
  54. ncbi request reprint New insights into clostridial neurotoxin-SNARE interactions
    Mark A Breidenbach
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Trends Mol Med 11:377-81. 2005
    ..New details regarding the nature of the toxin-SNARE interactions could be exploited for novel inhibitor design...
  55. ncbi request reprint The ENTH domain
    Pietro De Camilli
    Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
    FEBS Lett 513:11-8. 2002
    ..The ENTH domain is structurally similar to the VHS domain. These domains define two families of adaptor proteins which function in membrane traffic and whose interaction with membranes is regulated, in part, by phosphoinositides...
  56. ncbi request reprint Central pore residues mediate the p97/VCP activity required for ERAD
    Byron DeLaBarre
    Howard Hughes Medical Institute, Stanford University, JH Clark Center E300 C, California 94305, USA
    Mol Cell 22:451-62. 2006
    ..Except His317, which serves as an interaction nexus, these residues all lie on prominent loops within the D2 pore. These data support a model of substrate dislocation facilitated by interactions with p97/VCP's D2 pore...
  57. ncbi request reprint Considerations for the refinement of low-resolution crystal structures
    Byron DeLaBarre
    Howard Hughes Medical Institute, USA
    Acta Crystallogr D Biol Crystallogr 62:923-32. 2006
    ..Furthermore, large conformational changes can be discerned when structures in different states are available, information that is not easily obtainable by other means...
  58. ncbi request reprint Substrate recognition strategy for botulinum neurotoxin serotype A
    Mark A Breidenbach
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, USA
    Nature 432:925-9. 2004
    ..The novel structures of the substrate-recognition exosites could be used for designing inhibitors specific to BoNT/A...
  59. ncbi request reprint Automatic solution of heavy-atom substructures
    Charles M Weeks
    Hauptman Woodward Medical Research Institute, 73 High Street, Buffalo, New York 14203, USA
    Methods Enzymol 374:37-83. 2003
  60. pmc Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution
    Johannes Furst
    Howard Hughes Medical Institute and Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
    EMBO J 22:4365-74. 2003
    ..The density corresponding to alpha-SNAP and SNAREs is located on the 6-fold axis of the structure, near the NSF-N domains. The density of the N domain is weak, suggesting conformational variability in this part of NSF...
  61. ncbi request reprint Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle
    Isabelle Rouiller
    The Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Biol 9:950-7. 2002
    ..Taken together, our results depict the movements that this and possibly other AAA ATPases can undergo during an ATPase cycle...
  62. pmc Transmembrane signal transduction of the alpha(IIb)beta(3) integrin
    Kay E Gottschalk
    Institut fur Organische Chemie und Biochemie, Technische Universitat Munchen, Lichtenbergstrasse 4, D 85747 Garching, Germany
    Protein Sci 11:1800-12. 2002
    ..A transition between these two states was determined by molecular dynamics (MD) calculations. On the basis of these calculations, we propose a three-state mechanism...
  63. ncbi request reprint Domain flexibility in the 1.75 A resolution structure of Pb2+-calmodulin
    Mark A Wilson
    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02453, USA
    Acta Crystallogr D Biol Crystallogr 59:1782-92. 2003
    ....
  64. ncbi request reprint Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices
    Megan J Anderson
    Department of Biochemistry and Molecular Biophysics, California Institute of Technology, MS 128 95, Pasadena, California 91125, USA
    Biochemistry 46:5722-31. 2007
    ....
  65. ncbi request reprint Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states
    Charu Chaudhry
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 342:229-45. 2004
    ....
  66. ncbi request reprint Low-resolution crystallography is coming of age
    Axel T Brunger
    Structure 13:171-2. 2005
    ..8 to 4.7 A resolution. One of these structures, that of a fully glycosylated SIV gp120 envelope glycoprotein in an unliganded conformation at 4.0 A resolution, is described in this issue (Chen et al., 2005)...
  67. pmc Neuronal SNAREs do not trigger fusion between synthetic membranes but do promote PEG-mediated membrane fusion
    S Moses Dennison
    Department of Biochemistry and Program in Molecular Cell Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Biophys J 90:1661-75. 2006
    ..Thus, it is likely that proteins or factors other than the SNARE complex must trigger fusion in vivo...
  68. ncbi request reprint Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons
    James C Burnett
    Target Structure Based Drug Discovery Group, SAIC Frederick, Inc, Frederick, Maryland 21702, USA
    J Biol Chem 282:5004-14. 2007
    ..Isothermal titration calorimetry showed that the interaction between NSC 240898 and the botulinum A light chain is largely entropy-driven, and occurs with a 1:1 stoichiometry and a dissociation constant of 4.6 microM...

Research Grants9

  1. Single Molecule Studies of SNARE-Induced Vesicle Fusion
    AXEL BRUNGER; Fiscal Year: 2006
    ..Such a system could serve as an efficient model system for novel drug discovery. ..
  2. Single Molecule Studies of SNARE-Induced Vesicle Fusion
    AXEL BRUNGER; Fiscal Year: 2007
    ..Such a system could serve as an efficient model system for novel drug discovery. ..
  3. Single Molecule Studies of SNARE-Induced Vesicle Fusion
    AXEL BRUNGER; Fiscal Year: 2009
    ..Such a system could serve as an efficient model system for novel drug discovery. ..
  4. Single Molecule Studies of SNARE-Induced Vesicle Fusion
    Axel T Brunger; Fiscal Year: 2010
    ..Such a system could serve as an efficient model system for novel drug discovery. ..