B Rupp

Summary

Affiliation: Lawrence Livermore National Laboratory
Country: USA

Publications

  1. ncbi request reprint Predictive models for protein crystallization
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, University of California, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Methods 34:390-407. 2004
  2. ncbi request reprint Automated robotic harvesting of protein crystals-addressing a critical bottleneck or instrumentation overkill?
    Robert Viola
    Square One Systems Design, Jackson Hole, WY 83002, USA
    J Struct Funct Genomics 8:145-52. 2007
  3. ncbi request reprint Maximum-likelihood crystallization
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    J Struct Biol 142:162-9. 2003
  4. ncbi request reprint High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, California 94551, USA
    Acc Chem Res 36:173-81. 2003
  5. ncbi request reprint The TB structural genomics consortium crystallization facility: towards automation from protein to electron density
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Acta Crystallogr D Biol Crystallogr 58:1514-8. 2002
  6. ncbi request reprint Cloning, expression, and one-step purification of the minimal essential domain of the light chain of botulinum neurotoxin type A
    S Kadkhodayan
    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
    Protein Expr Purif 19:125-30. 2000
  7. ncbi request reprint The high-speed Hydra-Plus-One system for automated high-throughput protein crystallography
    Heike I Krupka
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Acta Crystallogr D Biol Crystallogr 58:1523-6. 2002
  8. pmc Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding
    B W Segelke
    Lawrence Livermore National Laboratory, Biology and Biotechnology Research Program, University of California, Livermore 94550, USA
    Protein Sci 9:886-97. 2000
  9. ncbi request reprint Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism
    P T Beernink
    Molecular and Structural Biology Division, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
    J Mol Biol 307:1023-34. 2001
  10. ncbi request reprint Laboratory scale structural genomics
    Brent W Segelke
    Macromolecular Crystallography and Structural Genomics Group, Biology and Biotechnology Research Program, P O Box 808, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    J Struct Funct Genomics 5:147-57. 2004

Collaborators

Detail Information

Publications29

  1. ncbi request reprint Predictive models for protein crystallization
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, University of California, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Methods 34:390-407. 2004
    ..Similar experimental design and knowledge discovery strategies should be applied to valid analysis and prediction of protein expression, solubilization, and purification, as well as crystal handling and cryo-protection...
  2. ncbi request reprint Automated robotic harvesting of protein crystals-addressing a critical bottleneck or instrumentation overkill?
    Robert Viola
    Square One Systems Design, Jackson Hole, WY 83002, USA
    J Struct Funct Genomics 8:145-52. 2007
    ....
  3. ncbi request reprint Maximum-likelihood crystallization
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    J Struct Biol 142:162-9. 2003
    ....
  4. ncbi request reprint High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, California 94551, USA
    Acc Chem Res 36:173-81. 2003
    ..Processes and methods presented in this review should assist academic institutions planning to invest in high-throughput structural biology to assess both the rewards and risks of establishing structural genomics programs...
  5. ncbi request reprint The TB structural genomics consortium crystallization facility: towards automation from protein to electron density
    Bernhard Rupp
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Acta Crystallogr D Biol Crystallogr 58:1514-8. 2002
    ..Modular design of robotics and automated scripts using publicly available programs for structure solution allow for efficient high throughput crystallography - at a reasonable cost...
  6. ncbi request reprint Cloning, expression, and one-step purification of the minimal essential domain of the light chain of botulinum neurotoxin type A
    S Kadkhodayan
    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
    Protein Expr Purif 19:125-30. 2000
    ..The purified protein was determined to be 98% pure as assessed by SDS-polyacrylamide gel. This protein has been crystallized and initial X-ray data show that the crystals diffract to 1.8 A...
  7. ncbi request reprint The high-speed Hydra-Plus-One system for automated high-throughput protein crystallography
    Heike I Krupka
    Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    Acta Crystallogr D Biol Crystallogr 58:1523-6. 2002
    ..The Hydra-Plus-One combines high precision, reliability and speed in a cost-effective high-throughput system ideally suited for protein crystallization..
  8. pmc Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding
    B W Segelke
    Lawrence Livermore National Laboratory, Biology and Biotechnology Research Program, University of California, Livermore 94550, USA
    Protein Sci 9:886-97. 2000
    ..This mobility at one end of the molecule provides new insights into the structural changes in apolipoprotein E that occur with lipid association...
  9. ncbi request reprint Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism
    P T Beernink
    Molecular and Structural Biology Division, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
    J Mol Biol 307:1023-34. 2001
    ..In conjunction, the structural and kinetic data suggest that Ape1 catalyzes hydrolysis of the DNA backbone through a two metal ion-mediated mechanism...
  10. ncbi request reprint Laboratory scale structural genomics
    Brent W Segelke
    Macromolecular Crystallography and Structural Genomics Group, Biology and Biotechnology Research Program, P O Box 808, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
    J Struct Funct Genomics 5:147-57. 2004
    ..The procedures are carried out by a small group using a combination of traditional approaches, innovative molecular biochemistry approaches, software automation, and a modest investment in robotic equipment...
  11. ncbi request reprint Novel mechanism for defective receptor binding of apolipoprotein E2 in type III hyperlipoproteinemia
    L M Dong
    Gladstone Institute of Cardiovascular Disease, University of California, San Francisco 94141 9100, USA
    Nat Struct Biol 3:718-22. 1996
    ..Our results demonstrate that defective binding of apoE2 occurs by a novel mechanism of the replacement of one salt bridge with another...
  12. ncbi request reprint Interaction of the N-terminal domain of apolipoprotein E4 with heparin
    J Dong
    Gladstone Institute of Cardiovascular Disease, Cardiovascular Research Institute, and Department of Pathology, University of California, San Francisco, California 94941-9100, USA
    Biochemistry 40:2826-34. 2001
    ..This prediction was confirmed experimentally by an observed increase in fluorescence intensity with octasaccharide binding corresponding to a K(d) of approximately 1 microM...
  13. pmc Crystal structure of Clostridium botulinum neurotoxin protease in a product-bound state: Evidence for noncanonical zinc protease activity
    Brent Segelke
    University of California, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA
    Proc Natl Acad Sci U S A 101:6888-93. 2004
    ..The proposed BoNT/A substrate-binding mode and catalytic mechanism are markedly different from those previously proposed for the BoNT serotype B...
  14. pmc Structural basis for abrogated binding between staphylococcal enterotoxin A superantigen vaccine and MHC-IIalpha
    Heike I Krupka
    Lawrence Livermore National Laboratory, Macromolecular Crystallography, Biology and Biotechnology Research Program, University of California, Livermore, California 94551, USA
    Protein Sci 11:642-51. 2002
    ..The triple-mutant structure provides new insights into the loss of superantigenicity and toxicity of an engineered superantigen and provides a basis for further design of enterotoxin vaccines...
  15. ncbi request reprint Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug target
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry and W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA
    Acta Crystallogr D Biol Crystallogr 61:355-64. 2005
    ..In silico screening of pyrimidine-nucleoside analogs has revealed a number of potential lead compounds that, if bound to Mtb pyrR, could facilitate transcriptional attenuation, particularly cyclopentenyl nucleosides...
  16. ncbi request reprint Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry and W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA
    Acta Crystallogr D Biol Crystallogr 60:895-902. 2004
    ..The 1.7 A native structure determined by the consortium facilities is reported and implications for in silico screening of ligands for structure-guided drug design are discussed...
  17. ncbi request reprint Protein isoelectric point as a predictor for increased crystallization screening efficiency
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, CA 92834 6866, USA
    Bioinformatics 20:2162-8. 2004
    ....
  18. ncbi request reprint Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service
    Vinod Reddy
    Biochemistry and Biophysics Department, Texas A and M University, 2128 TAMU, College Station, TX 77843 2128, USA
    Acta Crystallogr D Biol Crystallogr 59:2200-10. 2003
    ..Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures...
  19. ncbi request reprint Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis
    Kuppan Gokulan
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    J Biol Chem 278:18588-96. 2003
    ....
  20. ncbi request reprint The TB structural genomics consortium: providing a structural foundation for drug discovery
    Celia W Goulding
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Curr Drug Targets Infect Disord 2:121-41. 2002
    ..The Consortium has determined structures of 28 proteins from TB to date. These protein structures are already providing a basis for drug discovery efforts...
  21. ncbi request reprint Antibody elbow angles are influenced by their light chain class
    Robyn L Stanfield
    Department of Molecular Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 357:1566-74. 2006
    ..A new, web-based computer program that was used to calculate the Fab elbow angles is described...
  22. ncbi request reprint Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis
    Jean Denis Pédelacq
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Proteins 62:563-9. 2006
    ..The shape and size of the putative binding pocket is markedly different from that of members of the PNPOx family, which may indicate some significant changes in the FMN binding mode of this protein relative to members of the family...
  23. ncbi request reprint Mass spectrometric identification of serine hydrolase OVCA2 in the medulloblastoma cell line DAOY
    Amedeo A Azizi
    Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 19 21, A 1090 Vienna, Austria
    Cancer Lett 241:235-49. 2006
    ..In addition to the presence of OVCA2 in medulloblastoma, it was furthermore detectable in three out of 10 human tumour cell-lines as a high abundance protein probably suggesting a role in the tumour biology...
  24. ncbi request reprint Cocrystal structures of NC6.8 Fab identify key interactions for high potency sweetener recognition: implications for the design of synthetic sweeteners
    Kuppan Gokulan
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
    Biochemistry 44:9889-98. 2005
    ..Overall similarities and partial conservation of interactions indicate that the NC6.8 Fab surrogate is representing crucial features of the T1R2 taste receptor VFTM binding site...
  25. ncbi request reprint Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibility
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry, W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA
    Acta Crystallogr D Biol Crystallogr 58:735-43. 2002
    ..Suggestions on how to effectively represent ensembles of crystallographic models of a given molecule are provided...
  26. ncbi request reprint The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis
    Graeme L Card
    School of Biological Sciences, University of Auckland, Auckland, New Zealand
    J Biol Chem 280:13978-86. 2005
    ....
  27. ncbi request reprint Structural bioinformatic approaches to the discovery of new antimycobacterial drugs
    Katherine Kantardjieff
    W M Keck Foundation Center for Molecular Structure, Department of Chemistry and Biochemistry, California State University Fullerton, CA 92834 6866, USA
    Curr Pharm Des 10:3195-211. 2004
    ..In this review, we describe selected recent progress in antimycobacterial drug design, illustrating the strengths and limitations of current structural bioinformatic approaches as tools in the fight against tuberculosis...
  28. ncbi request reprint Apolipoprotein E4 forms a molten globule. A potential basis for its association with disease
    Julie A Morrow
    Gladstone Institutes of Cardiovascular Disease and Neurological Disease, San Francisco, California 94141 9100, USA
    J Biol Chem 277:50380-5. 2002
    ..Since molten globules have been implicated in both normal and abnormal physiological function, the differential abilities of the apoE isoforms to form a molten globule may contribute to the isoform-specific effects of apoE in disease...
  29. pmc Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry, California State University CSU Fullerton, Fullerton, California 92834 6866, USA
    Protein Sci 12:1865-71. 2003
    ....