David Eisenberg

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The amyloid state of proteins in human diseases
    David Eisenberg
    Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, Los Angeles CA 90095 1570, USA
    Cell 148:1188-203. 2012
  2. pmc Inferring protein domain interactions from databases of interacting proteins
    Robert Riley
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA
    Genome Biol 6:R89. 2005
  3. pmc Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
  4. pmc The structural biology of protein aggregation diseases: Fundamental questions and some answers
    David Eisenberg
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, Los Angeles, California 90095 1570, USA
    Acc Chem Res 39:568-75. 2006
  5. ncbi request reprint Protein function in the post-genomic era
    D Eisenberg
    Molecular Biology Institute and UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California at Los Angeles, 90095 1570, USA
    Nature 405:823-6. 2000
  6. ncbi request reprint Structure-function relationships of glutamine synthetases
    D Eisenberg
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Departments of Chemistry, Biochemistry and Biological Chemistry, University of California, Los Angeles, 201 MBI, Box 951570, Los Angeles, CA 90095 1570, USA
    Biochim Biophys Acta 1477:122-45. 2000
  7. ncbi request reprint John T. Edsall as tutor and teacher
    David Eisenberg
    Department of Biological Chemistry, Howard Hughes Medical Institute, Molecular Biology Institute, Box 951579, UCLA, Los Angeles, CA 90095 1570, USA
    Biophys Chem 100:91-3. 2003
  8. pmc Bioinformatic challenges for the next decade(s)
    David Eisenberg
    Howard Hughes Medical Institute UCLA DOE Institute for Genomics and Proteomics Box 951570 UCLA, Los Angeles, CA 90095 1570, USA
    Philos Trans R Soc Lond B Biol Sci 361:525-7. 2006
  9. pmc Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach
    Michael Strong
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Genome Biol 4:R59. 2003
  10. pmc The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins
    David Eisenberg
    Howard Hughes Medical Institute and University of California Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 100:11207-10. 2003

Research Grants

  1. A Core Database of Interacting Proteins (DIP)
    David Eisenberg; Fiscal Year: 2007
  2. Structural Biology of Amyloid Disease
    David Eisenberg; Fiscal Year: 2007
  3. A Core Database of Interacting Proteins (DIP)
    David Eisenberg; Fiscal Year: 2009
  4. Structural Biology of Amyloid Disease
    David Eisenberg; Fiscal Year: 2010
  5. A Core Database of Interacting Proteins
    David Eisenberg; Fiscal Year: 2010

Collaborators

Detail Information

Publications127 found, 100 shown here

  1. pmc The amyloid state of proteins in human diseases
    David Eisenberg
    Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, Los Angeles CA 90095 1570, USA
    Cell 148:1188-203. 2012
    ..Molecular studies have also led to numerous strategies for biological and chemical interventions against amyloid diseases...
  2. pmc Inferring protein domain interactions from databases of interacting proteins
    Robert Riley
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA
    Genome Biol 6:R89. 2005
    ..DPEA may prove useful in guiding experiment-based discovery of previously unrecognized domain interactions...
  3. pmc Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
    ....
  4. pmc The structural biology of protein aggregation diseases: Fundamental questions and some answers
    David Eisenberg
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, Los Angeles, California 90095 1570, USA
    Acc Chem Res 39:568-75. 2006
    ....
  5. ncbi request reprint Protein function in the post-genomic era
    D Eisenberg
    Molecular Biology Institute and UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California at Los Angeles, 90095 1570, USA
    Nature 405:823-6. 2000
    ....
  6. ncbi request reprint Structure-function relationships of glutamine synthetases
    D Eisenberg
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Departments of Chemistry, Biochemistry and Biological Chemistry, University of California, Los Angeles, 201 MBI, Box 951570, Los Angeles, CA 90095 1570, USA
    Biochim Biophys Acta 1477:122-45. 2000
    ..We review structural and functional studies of both bacterial and eukaryotic glutamine synthetases, with emphasis on enzymatic inhibitors...
  7. ncbi request reprint John T. Edsall as tutor and teacher
    David Eisenberg
    Department of Biological Chemistry, Howard Hughes Medical Institute, Molecular Biology Institute, Box 951579, UCLA, Los Angeles, CA 90095 1570, USA
    Biophys Chem 100:91-3. 2003
  8. pmc Bioinformatic challenges for the next decade(s)
    David Eisenberg
    Howard Hughes Medical Institute UCLA DOE Institute for Genomics and Proteomics Box 951570 UCLA, Los Angeles, CA 90095 1570, USA
    Philos Trans R Soc Lond B Biol Sci 361:525-7. 2006
    ..We here give a consideration of some of the key problems of bioinformatics in the coming decade, and perhaps longer...
  9. pmc Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach
    Michael Strong
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Genome Biol 4:R59. 2003
    ....
  10. pmc The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins
    David Eisenberg
    Howard Hughes Medical Institute and University of California Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 100:11207-10. 2003
    ..However, they did not consider the hand of the helix or the possibility of bent sheets. They also proposed structures and functions that have not been found, including the gamma-helix...
  11. ncbi request reprint Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis
    Celia W Goulding
    Howard Hughes Medical Institute and UCLA Department of Energy Institute of Genomics and Proteomics, Los Angeles, California 90095 1570
    J Biol Chem 279:3516-24. 2004
    ..Structural and biochemical analysis implies that Mtb DsbE functions differently from Gram-negative DsbE homologs, and we discuss its possible functional role in the bacterium...
  12. pmc Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin)
    Jed J W Wiltzius
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Los Angeles, California 90095 1570, USA
    Protein Sci 17:1467-74. 2008
    ..The atomic structures of these two segments, NNFGAIL and SSTNVG, were determined, and form the basis of a model for the most commonly observed, full-length IAPP polymorph...
  13. pmc Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps
    Michael Strong
    Howard Hughes Medical Institute, University of California at Los Angeles, Box 951570, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 31:7099-109. 2003
    ....
  14. pmc Structure of the cross-beta spine of amyloid-like fibrils
    Rebecca Nelson
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Box 951570, UCLA, Los Angeles, California 90095 1570, USA
    Nature 435:773-8. 2005
    ..The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures...
  15. pmc Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis
    Michael Strong
    Howard Hughes Medical Institute, UCLA Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 103:8060-5. 2006
    ..Our entire procedure for the identification, characterization, and structural determination of protein complexes can be scaled to a genome-wide level...
  16. pmc PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence
    Gary Kleiger
    Howard Hughes Medical Institute, University of California, Los Angeles Department Of Energy, Institute of Genomics and Proteomics, UCLA, Los Angeles, California 90095, USA
    Protein Sci 13:221-9. 2004
    ..Overall, we demonstrate that the structure-based PFIT and PFRIT algorithms are both more selective and sensitive for predicting glycosidase function than the sequence-based PSI-BLAST algorithm...
  17. pmc Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates
    Cong Liu
    UCLA DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 109:20913-8. 2012
    ..We propose that out-of-register β-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway...
  18. pmc The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold
    Zhefeng Guo
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA, Los Angeles, California 90095 1570, USA
    Protein Sci 17:1617-23. 2008
    ..We conclude that twisting of fibril forming sequences from the fully extended conformation, imposed by the context of their placement in proteins, can interfere with fibril formation...
  19. pmc Using inferred residue contacts to distinguish between correct and incorrect protein models
    Christopher S Miller
    UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Box 951570, UCLA, Los Angeles, CA 90095, USA
    Bioinformatics 24:1575-82. 2008
    ..can inter-residue contact predictions from multiple sequence alignments, information which is orthogonal to that used in most structure prediction algorithms, be used to identify those models most similar to the native protein structure?..
  20. ncbi request reprint The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function
    Celia W Goulding
    Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 1570, USA
    J Mol Biol 365:275-83. 2007
    ..We propose a novel enzymatic function for M. tuberculosis CitE in fatty acid biosynthesis that is analogous to bacterial citrate lyase but producing acetyl-CoA rather than a protein-bound CoA derivative...
  21. pmc Structure and assembly of an augmented Sm-like archaeal protein 14-mer
    Cameron Mura
    Howard Hughes Medical Institute, Molecular Biology Institute, and Department of Energy Institute for Genomics and Proteomics, 201 Boyer Hall Molecular Biology Institute, University of California, Box 951570, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 100:4539-44. 2003
    ..These results distinguish SmAP3s from other Sm proteins and provide a model for the structure and properties of Sm proteins >100 residues in length, e.g., several human Sm proteins...
  22. doi request reprint Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
    Stuart A Sievers
    Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Box 951970, Los Angeles, California 90095 1570, USA
    Nature 475:96-100. 2011
    ..Because the inhibiting peptides have been designed on structures of dual-β-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers...
  23. ncbi request reprint Atomic structures of amyloid cross-beta spines reveal varied steric zippers
    Michael R Sawaya
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, Los Angeles, California 90095 1570, USA
    Nature 447:453-7. 2007
    ..Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains...
  24. pmc Atomic structures suggest determinants of transmission barriers in mammalian prion disease
    Marcin I Apostol
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, UCLA DOE Institute, UCLA, 611 Charles Young Drive East, Los Angeles, California 90095 1570, United States
    Biochemistry 50:2456-63. 2011
    ....
  25. pmc The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg²⁺ ion in the active site and a putative RNA-binding site
    Andrew B Min
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, California 90095 1570, USA
    Protein Sci 21:1754-67. 2012
    ....
  26. doi request reprint Atomic view of a toxic amyloid small oligomer
    Arthur Laganowsky
    Department of Biological Chemistry, University of California Los Angeles UCLA, Howard Hughes Medical Institute HHMI, Los Angeles, CA 90095, USA
    Science 335:1228-31. 2012
    ..The cylindrin structure is compatible with a sequence segment from the β-amyloid protein of Alzheimer's disease. Cylindrins offer models for the hitherto elusive structures of amyloid oligomers...
  27. pmc Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression
    Einat Sprinzak
    UCLA DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
    BMC Syst Biol 3:115. 2009
    ..However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships...
  28. ncbi request reprint Utilizing logical relationships in genomic data to decipher cellular processes
    Peter M Bowers
    Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
    FEBS J 272:5110-8. 2005
    ....
  29. pmc Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process
    Jed J W Wiltzius
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, Los Angeles, California 90095 1570, USA
    Protein Sci 18:1521-30. 2009
    ..Taken together, these experiments suggest the helical dimerization of IAPP accelerates fibril formation and that insulin impedes fibrillation by blocking the IAPP dimerization interface...
  30. pmc Molecular mechanisms for protein-encoded inheritance
    Jed J W Wiltzius
    UCLA DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Molecular Biology Institute, University of California, Los Angeles, California, USA
    Nat Struct Mol Biol 16:973-8. 2009
    ....
  31. pmc A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments
    Magdalena I Ivanova
    Howard Hughes Medical Institute and University of California Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 103:4079-82. 2006
    ....
  32. ncbi request reprint Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA
    Celia W Goulding
    UCLA DOE Center for Genomics and Proteomics, UCLA Box 951570, Los Angeles, CA 90095 1570, USA
    Biophys Chem 105:361-70. 2003
    ..tuberculosis structural genomics project will yield information for drug design and vaccine production against tuberculosis. In addition, this study will provide further insights into the mechanisms of mycobacterial pathogenesis...
  33. pmc Prolinks: a database of protein functional linkages derived from coevolution
    Peter M Bowers
    Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Genome Biol 5:R35. 2004
    ..The Prolinks database and the Proteome Navigator tool are available for use online at http://dip.doe-mbi.ucla.edu/pronav...
  34. pmc The 3D profile method for identifying fibril-forming segments of proteins
    Michael J Thompson
    Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 103:4074-8. 2006
    ..We see enrichment for positive predictions in a set of fibril-forming segments of amyloid proteins, and we illustrate the method with applications to proteins of interest in amyloid research...
  35. pmc Molecular basis for insulin fibril assembly
    Magdalena I Ivanova
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Los Angeles CA 90095 1570, USA
    Proc Natl Acad Sci U S A 106:18990-5. 2009
    ..This structure leads to a model for fibrils of human insulin consistent with electron microscopic, x-ray fiber diffraction, and biochemical studies...
  36. pmc Short protein segments can drive a non-fibrillizing protein into the amyloid state
    Poh K Teng
    Department of Biological Chemistry, UCLA DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Molecular Biology Institute, UCLA, Box 951570, Los Angeles, CA 90095 1570, USA
    Protein Eng Des Sel 22:531-6. 2009
    ..These six to eight residue inserts can fibrillize RNase A and are sufficient for amyloid fibril spine formation...
  37. ncbi request reprint Structure and function of an archaeal homolog of survival protein E (SurEalpha): an acid phosphatase with purine nucleotide specificity
    Cameron Mura
    Howard Hughes Medical Institute and UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, 201 Boyer Hall, Box 951570, Los Angeles, CA 90095 1570, USA
    J Mol Biol 326:1559-75. 2003
    ....
  38. ncbi request reprint Use of logic relationships to decipher protein network organization
    Peter M Bowers
    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Science 306:2246-9. 2004
    ..These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins...
  39. ncbi request reprint The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase
    Peter Muller
    UCLA DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Box 951570, Los Angeles, CA 90095 1570, USA
    Acta Crystallogr D Biol Crystallogr 61:309-15. 2005
    ..These segments lie on the enzyme surface and could conceivably participate in protein-protein interactions...
  40. ncbi request reprint Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme
    Celia W Goulding
    Molecular Biology Institute UCLA DOE Institute of Genomics and Proteomics, P O Box 951570, Los Angeles, CA 90095 1570, USA
    J Mol Biol 349:61-72. 2005
    ..tuberculosis against host defenses...
  41. ncbi request reprint Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure
    Shilpa Sambashivan
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Box 951570, UCLA, Los Angeles, California 90095 1570, USA
    Nature 437:266-9. 2005
    ..These findings are consistent with the zipper-spine model in which a cross-beta spine is decorated with three-dimensional domain-swapped functional units, retaining native-like structure...
  42. ncbi request reprint Detection of parallel functional modules by comparative analysis of genome sequences
    Huiying Li
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, 90095 1570, USA
    Nat Biotechnol 23:253-60. 2005
    ..The approach untangles intertwined functional linkages between parallel functional modules and expands our ability to decode protein functions from genome sequences...
  43. ncbi request reprint Inference of protein function from protein structure
    Debnath Pal
    UCLA DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
    Structure 13:121-30. 2005
    ..Overall, about 70% of the assignments were inferred correctly. This level of performance suggests that ProKnow is a useful resource in functional assessments of novel proteins...
  44. pmc Molecular basis for amyloid-beta polymorphism
    Jacques Philippe Colletier
    Howard Hughes Medical Institute, Department of Biological Chemistry and Chemistry and Biochemistry, UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 108:16938-43. 2011
    ..These structures and molecular models contribute fundamental information for understanding Aβ polymorphic nature and pathogenesis...
  45. pmc A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms
    Michael R Sawaya
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, Los Angeles, CA 90095, USA
    Cell 134:1007-18. 2008
    ..These studies provide insight into how "matching" at all three pairs of variable domains in Dscam mediates isoform-specific recognition...
  46. ncbi request reprint Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning
    Sangho Lee
    UCLA DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Howard Hughes Medical Institute, and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Acta Crystallogr D Biol Crystallogr 59:2191-9. 2003
    ..The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme...
  47. ncbi request reprint Granulysin crystal structure and a structure-derived lytic mechanism
    Daniel H Anderson
    Howard Hughes Medical Institute, 5 748 MacDonald, Box 951662, Los Angeles, CA 90095 1662, USA
    J Mol Biol 325:355-65. 2003
    ..The loosely packed core facilitates a hinge or scissors motion towards exposure of hydrophobic surface that we propose tunnels the granulysin into the fracturing target membrane...
  48. pmc Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function
    Arthur Laganowsky
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Los Angeles, California, USA
    Protein Sci 19:1031-43. 2010
    ..This evolved polydispersity suggests molecular mechanisms for chaperone action and for prevention of crystallization, both necessary for transparency of eye lenses...
  49. pmc Towards a pharmacophore for amyloid
    Meytal Landau
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California, United States of America
    PLoS Biol 9:e1001080. 2011
    ..In contrast, negatively charged orange-G binds specifically to lysine side chains of adjacent sheets. These structures provide molecular frameworks for the design of diagnostics and drugs for protein aggregation diseases...
  50. pmc Toward rational protein crystallization: A Web server for the design of crystallizable protein variants
    Lukasz Goldschmidt
    Howard Hughes Medical Institute, University of California, Los Angeles DOE Institute of Genomics and Proteomics, Los Angeles, California 90095 1570, USA
    Protein Sci 16:1569-76. 2007
    ..In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER...
  51. pmc The Database of Interacting Proteins: 2004 update
    Lukasz Salwinski
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, 90095 1570, USA
    Nucleic Acids Res 32:D449-51. 2004
    ....
  52. pmc Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease
    Marcin I Apostol
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA DOE Institute, UCLA, Los Angeles, California 90095 1570, USA
    J Biol Chem 285:29671-5. 2010
    ..These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression...
  53. ncbi request reprint Functional linkages can reveal protein complexes for structure determination
    Sul Min Kim
    Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
    Structure 15:1079-89. 2007
    ..We offer a database of inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archaea...
  54. pmc Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis
    Linda Miallau
    UCLA DOE Institute of Genomics and Proteomics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095 1570, USA
    J Biol Chem 284:276-83. 2009
    ..Furthermore, analysis of the interactions in the binding of the antitoxin to the toxin suggest that exquisite control is required to protect the bacteria cell from toxic VapC-5...
  55. pmc An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril
    Magdalena I Ivanova
    Howard Hughes Medical Institute and University of California Department of Energy Institute of Genomics and Proteomics, Box 951570, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:10584-9. 2004
    ..These observations are consistent with a proposed Zipper-spine model for beta2M amyloid, in which the spine of the fibril consists of an anhydrous beta-sheet...
  56. pmc Identifying the amylome, proteins capable of forming amyloid-like fibrils
    Lukasz Goldschmidt
    Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 107:3487-92. 2010
    ..The implication is that chaperoning effects have evolved to constrain self-complementary segments from interaction with each other...
  57. pmc Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution
    Celia W Goulding
    Howard Hughes Medical Institute, University of California at Los Angeles DOE, Center for Genomics and Proteomics, Los Angeles 90095, USA
    Protein Sci 11:2887-93. 2002
    ..Although the structure of MPT63 gives no conclusive evidence to its function, structural similarity suggests that MPT63 could be involved in cell-host interactions to facilitate endocytosis/phagocytosis...
  58. pmc Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I
    Zhefeng Guo
    Howard Hughes Medical Institute, University of California, Los Angeles Department of Energy Institute for Genomics and Proteomics, Molecular Biology Institute, Box 951570, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 103:8042-7. 2006
    ..In addition, our results suggest that inhibition of fibril formation for domain-swapped proteins may be achieved by stabilizing domain-swapped dimers...
  59. ncbi request reprint The protein network as a tool for finding novel drug targets
    Michael Strong
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics and Proteomics, University of California Los Angeles, USA
    Prog Drug Res 64:191, 193-215. 2007
    ..In this chapter we discuss methods for the identification and analysis of genome-wide protein networks, and discuss how protein networks can be used to aid the identification of novel drug targets...
  60. ncbi request reprint Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum
    Huiying Li
    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Box 951570, Los Angeles, California 90095, USA
    Structure 13:779-89. 2005
    ..Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis...
  61. pmc Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide
    Jing Zheng
    Department of Chemistry, University of California, Irvine, Irvine, California 92697 2025, USA
    J Am Chem Soc 133:3144-57. 2011
    ..This model provides a provocative and appealing target for future inhibitor design...
  62. pmc The crystal structure of the Mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer
    Mark A Arbing
    UCLA DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 1570, USA
    Protein Sci 19:1692-703. 2010
    ....
  63. pmc The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds
    Parag Mallick
    Department of Chemistry and Biochemistry, and University of California, UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 99:16041-6. 2002
    ....
  64. pmc Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic β-sheet mimics
    Cong Liu
    UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
    J Am Chem Soc 133:6736-44. 2011
    ....
  65. pmc Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate
    Shuishu Wang
    Howard Hughes Medical Institute, UCLA DOE Institute of Genomics, Molecular Biology Institute, University of California, Los Angeles, 90095 1570, USA
    Protein Sci 12:1097-108. 2003
    ..The tight binding of the intermediate pantoyl adenylate suggests that nonreactive analogs of pantoyl adenylate may be inhibitors of the PS enzyme with high affinity and specificity...
  66. ncbi request reprint Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response
    Philip T Liu
    Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA 90095, USA
    Science 311:1770-3. 2006
    ..These data support a link between TLRs and vitamin D-mediated innate immunity and suggest that differences in ability of human populations to produce vitamin D may contribute to susceptibility to microbial infection...
  67. ncbi request reprint Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD
    Celia W Goulding
    Howard Hughes Medical Institute and Laboratory of Structural Biology and Molecular Medicine, UCLA DOE, P O Box 951570, Los Angeles, California 90095 1570, USA
    Biochemistry 41:6920-7. 2002
    ..A model is discussed whereby the immunoglobulin fold of DsbD(N) may provide for the discriminating interaction with thioredoxin-like factors, thereby triggering movement of the phenylalanine cap followed by disulfide rearrangement...
  68. pmc Structures of segments of α-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation
    Minglei Zhao
    Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Protein Sci 20:996-1004. 2011
    ..Our structures suggest intermediate states during amyloid formation of α-synuclein...
  69. ncbi request reprint The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins
    Lukasz Salwinski
    UCLA DOE Institute for Genomics and Proteomics, Department of Chemistry, Howard Hughes Medical Institute, Box 951570, UCLA, Los Angeles, CA 90095, USA
    Bioinformatics 23:2193-5. 2007
    ..Availability: MiSink is freely available for download at http://dip.doe-mbi.ucla.edu/Software.cgi...
  70. pmc The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue
    Tsungda Hsu
    Howard Hughes Medical Institute, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 100:12420-5. 2003
    ..We conclude that the primary attenuating mechanism of bacillus Calmette-Guérin is the loss of cytolytic activity mediated by secreted ESAT-6, which results in reduced tissue invasiveness...
  71. pmc X-ray crystallographic structure of an artificial beta-sheet dimer
    Omid Khakshoor
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Am Chem Soc 132:11622-8. 2010
    ....
  72. ncbi request reprint Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database
    Xiaoqun Joyce Duan
    Howard Hughes Medical Institute, UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, Los Angeles, California 90095 1570, USA
    Mol Cell Proteomics 1:104-16. 2002
    ..These examples illustrate how LiveDIP provides data and tools for biological pathway discovery and pathway analysis...
  73. ncbi request reprint The mechanism of the amyloidogenic conversion of T7 endonuclease I
    Zhefeng Guo
    Howard Hughes Medical Institute, UCLA Department of Energy Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA, Los Angeles, California 90095 1570, USA
    J Biol Chem 282:14968-74. 2007
    ..In this model, some amyloid-enhancing mutations decrease protein stability, whereas others have little effect...
  74. ncbi request reprint Use of genetic profiling in leprosy to discriminate clinical forms of the disease
    Joshua R Bleharski
    Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at University of California Los Angeles UCLA, Los Angeles, CA 90095, USA
    Science 301:1527-30. 2003
    ..Gene expression profiles may be useful in defining clinical forms of disease and providing insights into the regulation of immune responses to pathogens...
  75. ncbi request reprint DPANN: improved sequence to structure alignments following fold recognition
    Astrid Reinhardt
    Faint Signals Pattern Recognition, Los Angeles, California, USA
    Proteins 56:528-38. 2004
    ..In the artificial case of using actual instead of predicted secondary structures for the probe protein, over 50% of the alignments are successful...
  76. pmc DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    Ioannis Xenarios
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, PO Box 951570, UCLA, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 30:303-5. 2002
    ..Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database...
  77. ncbi request reprint Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
    R Landgraf
    UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 405 Hilgard Avenue, Los Angeles, CA, 90095-1570, USA
    J Mol Biol 307:1487-502. 2001
    ..These residue clusters correlate with specificity-conferring regions: 3D cluster analysis therefore represents an easily applied method for the prediction of functionally relevant spatial clusters of residues in proteins...
  78. pmc Structures of the two 3D domain-swapped RNase A trimers
    Yanshun Liu
    Howard Hughes Medical Institute, UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry, University of California, Los Angeles, California 90095, USA
    Protein Sci 11:371-80. 2002
    ..These structures permit interpretation of the enzymatic activities of the RNase A oligomers on double-stranded RNA...
  79. ncbi request reprint Computational methods of analysis of protein-protein interactions
    Lukasz Salwinski
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Departments of Chemistry and Biochemistry and Biological Chemistry, Molecular Biology Institute, Box 951570, UCLA, Los Angeles, CA 90095 1570, USA
    Curr Opin Struct Biol 13:377-82. 2003
    ..They are used to predict potential interactions, to validate the results of high-throughput interaction screens and to analyze the protein networks inferred from interaction databases...
  80. ncbi request reprint Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes
    R L Fahrner
    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
    Chem Biol 3:543-50. 1996
    ..They are composed of 16-18 amino-acid residues including four cysteines, which form two disulfide linkages. To begin to understand the mechanism of action of these peptides, we set out to determine the structure of protegrin-1 (PG-1)...
  81. ncbi request reprint The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition
    H S Gill
    UCLA DOE Lab of Structural Biology and Molecular Medicine, Box 951570, University of California, Los Angeles, California 90095 1570, USA
    Biochemistry 40:1903-12. 2001
    ..The inhibition of GS by methionine sulfoximine can be explained by the same mechanism. These models of inhibited GS further illuminate its catalytic mechanism...
  82. pmc Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold
    M Wilmanns
    Molecular Biology Institute, University of California, Los Angeles 90024 1570
    Proc Natl Acad Sci U S A 90:1379-83. 1993
    ....
  83. ncbi request reprint Protein interaction databases
    I Xenarios
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, PO Box 951570, Los Angeles, CA 90095 1570, USA
    Curr Opin Biotechnol 12:334-9. 2001
    ..These databases document, categorize, and analyze interacting proteins and the cellular functions of the interactions...
  84. ncbi request reprint An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B), a mycolyl transferase
    D H Anderson
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, CA 90095 1570, USA
    J Mol Biol 307:671-81. 2001
    ..Based on the trehalose-bound structure, we suggest a new class of antituberculous drugs, made by connecting two trehalose molecules by an amphipathic linker...
  85. ncbi request reprint Fold assignments for amino acid sequences of the CASP2 experiment
    D W Rice
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine 90095 1570, USA
    Proteins . 1997
    ....
  86. ncbi request reprint Recent atomic models of amyloid fibril structure
    Rebecca Nelson
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Box 951570, UCLA, Los Angeles, CA 90095 1570, USA
    Curr Opin Struct Biol 16:260-5. 2006
    ..The gain-of-interaction models may additionally be subdivided into direct stacking, cross-beta spine, three-dimensional domain swapping and three-dimensional domain swapping with a cross-beta spine...
  87. ncbi request reprint Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation
    Harindarpal S Gill
    Howard Hughes Medical Institute, UCLA Department of Energy Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry and Biochemistry, Box 951570, University of California, Los Angeles, CA 90095 1570, USA
    Biochemistry 41:9863-72. 2002
    ....
  88. ncbi request reprint Refined atomic model of glutamine synthetase at 3.5 A resolution
    M M Yamashita
    Molecular Biology Institute, University of California, Los Angeles 90024
    J Biol Chem 264:17681-90. 1989
    ..The central loop, which extends into the central aqueous channel, is subject to attack by at least five enzymes and is discussed as an enzyme "passive site."..
  89. ncbi request reprint Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization
    C P Hill
    Eisenberg, Molecular Biology Institute, Los Angeles, CA
    Science 251:1481-5. 1991
    ..19) reveals a dimeric beta sheet that has an architecture very different from other lytic peptides. The dimeric assembly suggests mechanisms by which defensins might bind to and permeabilize the lipid bilayer...
  90. ncbi request reprint Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution
    L J Beamer
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
    Science 276:1861-4. 1997
    ..As a model for the related plasma lipid transfer proteins, BPI illuminates a mechanism of lipid transfer for this protein family...
  91. ncbi request reprint A model for oxidative modification of glutamine synthetase, based on crystal structures of mutant H269N and the oxidized enzyme
    S H Liaw
    Molecular Biology Institute, University of California, Los Angeles 90024
    Biochemistry 32:7999-8003. 1993
    ..These studies also illuminate the differing roles of the two bound metal ions: the tightly bound n1 ion enhances the stability of the catalytically active conformation, and the less tightly bound n2 ion participates in ATP binding...
  92. ncbi request reprint The origin of protein interactions and allostery in colocalization
    John Kuriyan
    Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 450:983-90. 2007
    ..Thus, the regulated protein networks of organisms seem to be the inevitable consequence of natural selection operating under physical laws...
  93. ncbi request reprint Structural models of amyloid-like fibrils
    Rebecca Nelson
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, USA
    Adv Protein Chem 73:235-82. 2006
    ....
  94. pmc 3D domain swapping: as domains continue to swap
    Yanshun Liu
    Howard Hughes Medical Institute, UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry and Biochemistry and Biological Chemistry, University of California, Los Angeles, California 90095, USA
    Protein Sci 11:1285-99. 2002
    ..As domains continue to swap, this review attempts not only a summary of the known domain-swapped proteins, but also a framework for understanding future findings of 3D domain swapping...
  95. ncbi request reprint Deposition diseases and 3D domain swapping
    Melanie J Bennett
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
    Structure 14:811-24. 2006
    ....
  96. pmc Feedback inhibition of fully unadenylylated glutamine synthetase from Salmonella typhimurium by glycine, alanine, and serine
    S H Liaw
    Molecular Biology Institute, University of California, Los Angeles 90024
    Proc Natl Acad Sci U S A 90:4996-5000. 1993
    ..Thus on the basis of our x-ray work, glycine, alanine, and serine appear to inhibit GS-Mn by competing with the substrate glutamate for the active site...
  97. pmc Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis
    P J Hart
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles 90095, USA
    Protein Sci 7:545-55. 1998
    ..This structure is the first CuZnSOD to show large differences between the two subunits. Factors that may contribute to these differences are discussed and a possible link of a looser structure to FALS is suggested...
  98. ncbi request reprint Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide
    C E Bell
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, USA
    Biochemistry 35:1137-49. 1996
    ..Structural alignments of the DT-NAD complex with the structures of other members of the ADP-RT family suggest how NAD may bind to these other enzymes...
  99. pmc Motif-based fold assignment
    L Salwinski
    Department of Chemistry, UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, UCLA, Los Angeles, California 90095-1570, USA
    Protein Sci 10:2460-9. 2001
    ..The method is available through the web server localized at http://www.doe-mbi.ucla.edu/mba...
  100. ncbi request reprint Analysis of heregulin symmetry by weighted evolutionary tracing
    R Landgraf
    University of California, UCLA DOE Laboratory of Structural Biology and Molecular Medicine and Molecular Biology Institute, 405 Hilgard Avenue, Box 951570, Los Angeles, CA 90095 1570, USA
    Protein Eng 12:943-51. 1999
    ..This pseudo-twofold symmetry and the presence of two distinct interfaces may reflect the preference of hrg for heterodimeric versus homodimeric HER complexes...
  101. pmc Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing
    P Mallick
    UCLA DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry and Biochemistry, Molecular Biology Institute, Box 951570, University of California, Los Angeles, CA 90095 1570, USA
    Proc Natl Acad Sci U S A 97:2450-5. 2000
    ..Results of these studies have been collated and placed at http://www.doe-mbi.ucla.edu/people/parag/P A_HOME/, the University of California, Los Angeles-Department of Energy Pyrobaculum aerophilum web site...

Research Grants9

  1. A Core Database of Interacting Proteins (DIP)
    David Eisenberg; Fiscal Year: 2007
    ..To provide faster and more reliable access to DIP, its IT infrastructure will be upgraded. ..
  2. Structural Biology of Amyloid Disease
    David Eisenberg; Fiscal Year: 2007
    ..These structures offer a solid foundation on which to devise diagnostics and therapeutics for these devastating neurodegenerative diseases. ..
  3. A Core Database of Interacting Proteins (DIP)
    David Eisenberg; Fiscal Year: 2009
    ..To provide faster and more reliable access to DIP, its IT infrastructure will be upgraded. ..
  4. Structural Biology of Amyloid Disease
    David Eisenberg; Fiscal Year: 2010
    ..These structures offer a solid foundation on which to devise diagnostics and therapeutics for these devastating neurodegenerative diseases. ..
  5. A Core Database of Interacting Proteins
    David Eisenberg; Fiscal Year: 2010
    ..DIP is a free and open community resource for research physicians and scientists. DIP takes special care in documenting the accuracy of the data it contains. ..