Research Topics
| B RuppSummaryAffiliation: Lawrence Livermore National Laboratory Country: USA Publications
| Collaborators
|
Detail Information
Publications
Predictive models for protein crystallizationBernhard 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...- 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.... - Maximum-likelihood crystallizationBernhard Rupp
Macromolecular Crystallography and TB Structural Genomics Consortium, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
J Struct Biol 142:162-9. 2003.... - High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization FacilityBernhard 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... - The TB structural genomics consortium crystallization facility: towards automation from protein to electron densityBernhard 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... - Cloning, expression, and one-step purification of the minimal essential domain of the light chain of botulinum neurotoxin type AS 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... - The high-speed Hydra-Plus-One system for automated high-throughput protein crystallographyHeike 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.. 
Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid bindingB 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...- Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanismP 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... - Laboratory scale structural genomicsBrent 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... - Novel mechanism for defective receptor binding of apolipoprotein E2 in type III hyperlipoproteinemiaL 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... - Interaction of the N-terminal domain of apolipoprotein E4 with heparinJ 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... - Crystal structure of Clostridium botulinum neurotoxin protease in a product-bound state: Evidence for noncanonical zinc protease activityBrent 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... - Structural basis for abrogated binding between staphylococcal enterotoxin A superantigen vaccine and MHC-IIalphaHeike 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... - Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug targetKatherine 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... - Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathwayKatherine 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... - Protein isoelectric point as a predictor for increased crystallization screening efficiencyKatherine A Kantardjieff
Department of Chemistry and Biochemistry, California State University Fullerton, Fullerton, CA 92834 6866, USA
Bioinformatics 20:2162-8. 2004.... - Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web ServiceVinod 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... - Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesisKuppan Gokulan
Department of Biochemistry and Biophysics, Texas A and M University, College Station, Texas 77843 2128, USA
J Biol Chem 278:18588-96. 2003.... - The TB structural genomics consortium: providing a structural foundation for drug discoveryCelia 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... - Antibody elbow angles are influenced by their light chain classRobyn 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... - Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosisJean 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... - Mass spectrometric identification of serine hydrolase OVCA2 in the medulloblastoma cell line DAOYAmedeo 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... - Cocrystal structures of NC6.8 Fab identify key interactions for high potency sweetener recognition: implications for the design of synthetic sweetenersKuppan 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... - Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibilityKatherine 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... - 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 biosynthesisGraeme L Card
School of Biological Sciences, University of Auckland, Auckland, New Zealand
J Biol Chem 280:13978-86. 2005.... - Structural bioinformatic approaches to the discovery of new antimycobacterial drugsKatherine 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... - Apolipoprotein E4 forms a molten globule. A potential basis for its association with diseaseJulie 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... - Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystalsKatherine A Kantardjieff
Department of Chemistry and Biochemistry, California State University CSU Fullerton, Fullerton, California 92834 6866, USA
Protein Sci 12:1865-71. 2003....