PEOPLE

David Eisenberg » Bio/CV

Curriculum Vitae

DAVID EISENBERG

Education
Harvard College,
Cambridge, MA		 A. B 1961 Biochemical Sciences
(John Edsall)
Oxford University,
Oxford, England		 D. Phil. 1964 Theoretical Chemistry
(Charles Coulson)

Professional Experience
Princeton University,
Princeton, NJ		 Postdoc 1964-1966 Water, H-bonding
(Walter Kauzmann)
California Institute of Technology,
Pasadena, CA		 Postdoc 1966-1969 Structural Biology
(Richard Dickerson)
University of California,
Los Angeles, CA		 Asst. Professor-
Professor		 1969-present Chemistry & Biochemistry, Molecular Biology
University of California,
Los Angeles, CA		 Director 1993-present UCLA-DOE Institute for Genomics & Proteomics
Howard Hughes Medical Institute Investigator 2001-present  

Awards

L.J. Henderson Prize, 1961; Harvard College Honorary Scholarships, 1958-1960; Phi Beta Kappa; Sigma Xi; Rhodes Scholarship, 1961-1964; Alfred P. Sloan Fellowship, 1969-1971; USPHS Career Development Award, 1972-1977; UCLA Distinguished Teaching Award, 1975; McCoy Award of the UCLA Department of Chemistry and Biochemistry for innovative research, 1982 (with R.E. Dickerson); Guggenheim Fellowship, 1985; UCLA Faculty Research Lectureship, 1989; National Academy of Sciences, 1989; American Academy of Arts & Sciences, 1991; Pierce Award of the Immunotoxin Society, 1992; Protein Society Stein & Moore Award, 1996; American Chemical Society Repligen Award in Molecular Biology, 1998; Fellow, Biophysical Society, 1999; Amgen Award of the Protein Society, 2000; Fellow, American Association for the Advancement of Science, 2001; Institute of Medicine, 2002; American Philosophical Society, 2003; UCLA Seaborg Medal, 2004; Harvard Westheimer Medal, 2005.

Lectureships

Lawrence J. Onclay Lectureship, 1986 (University of Michigan); Henry Bull Lectureship, 1987 (University of Iowa); The Pfizer Lectureship, 1988 (Harvard); Faculty Research Lectureship, 1989 (UCLA); Karling Lecture, 1990 (Purdue); John T. Edsall Lectureship, 1992 (Harvard); University Lecturer, 1996 (UTSW, Dallas); Keynote address: Program in Mathematics & Molecular Biology, 1995 (Santa Fe); FMC Lectureship (Princeton), 1996; Biophysical Society National Lecture, 1997; National Lecturer, Diphtheria Toxin and Domain Swapping: A Strange Biophysical Tail, Biophysical Society Annual Meeting, 1997 (New Orleans); NIH Director's Seminar, "Protein-protein interactions", 1998 (Bethesda, MD); 16th Annual Hans Neurath Lecture, “Protein-Protein Interactions”, 1999 (University of Washington, Seattle, WA.); Inaugural Sunesis Lecture: "From Genome Sequences to Protein Functions", 2000 (UC Berkeley); Keynote lecture: World Congress of Bioinformatics, 2001 (Tokyo, Japan); Keynote address, Keystone Conference on Genomics and Structural Biology, 2002; Keynote address, Mid-Atlantic Protein Crystallographic Workshop, 2002; Keynote address at Maps, Sequences, and Genomes, a symposium in honor of Michael Waterman's 60th birthday, USC, 2002 (Los Angeles); Opening Keynote, Gordon Research Conference on Proteins, 2002 (New Hampshire); Opening plenary lecture: 17th Symposium of the Protein Society, 2002 (Boston, MA); Keynote address, Gordon Research Conference on Protein Folding Dynamics, 2004; Opening lecture, Royal Society Discussion on Bioinformatics, 2005 (London, UK); Seminar, Laboratory of Molecular Biology, 2005 (Cambridge UK); Keynote lecture, Faltertag 2005, (Wittenburg, Germany); Keynote, Kech Distinguished Scholars Retreat, 2005 (Los Angeles); Keynote address, 2005 (International Union of Crystallography XX, Florence, Italy); Keynote address: SPINE (Structural Genomics in Europe), 2005 (Montecatini Termi, Italy); Inaugural Robert L. Davis Lecture, 2005 (University of Arizona); The Cynthia Ann Chan Lecture, UC Berkeley: Protein Aggregation Diseases, 2006 (Berkeley, CA).

Selected Professional Activities

President, Protein Society, 1987-1989; Editor, Advances in Protein Chemistry, 1988-present; Editorial Advisory Board, Current Opinion in Biology, 1989-present; Editorial Consultant, Protein Science, 1991-1997; Guest Scientist, Brookhaven National Laboratory, 1993; University of Washington, NSF Center for Molecular Biotechnology, Advisory Committee, 1994-1998; Chair, Protein Data Bank Advisory Board, 1995-1999; Brookhaven National Lab, Biology Dept., Advisory Committee, 1996-1998; National Academy of Sciences, Class II Member-at-Large, Class Membership Committee, 1996-1998; National Research Council, Board of Biology, 1995-1998; IUPAC, Commission of Biophysical Chemistry, Associate Member, 1996-1999; Hereditary Disease Foundation, Scientific Advisory Board, 1996-present; National Research Council, Commission on Life Sciences, 1998-2001; Chair, NIH Ad hoc Committee on Structural Genomics, 1998; Protein Society Long Range Planning Committee, 1997-1999, Chair 1998; Chair, NIH NIGMS Ad Hoc Committee on Structural Genomics, 1998; Scientific Advisory Committee, European Molecular Biology Lab, 2000-2005; Scientific Advisory Board, Institute of Systems Biology, 2000-Present; Chair, Review of European Bioinformatics Institute, 2003; National Academy of Sciences: Organizing Chair, NAS Biophysics Section, 2001-2004; Member, NAS Committee on Community Standards for Sharing Publication-Related Data and Materials, 2002. Advisory Committee, Swiss National Science Foundation Center of Excellence in Structural Biology, 2002-2007; LBL Physical Biosciences Director's Division Review, May, 2003; Chair, Review of European Bioinformatics Institute, 2003; Petra Synchrotron Review Committee, 2004; Review Panel: Centre for Protein Engineering, LMB, Cambridge, UK, 2004. SAB, Harvard University Bauer Center, 2005-Present; SAB, BioDesign Institute, Arizona State University, 2006-9

Recent Research Publications

  1. “An Amyloid-forming Peptide from the Yeast Prion Sup35 Reveals a Dehydrated Beta-Sheet Structure for Amyloid” Balbirnie, M., Grothe, R., and Eisenberg, D. , PNAS, 98, 2375-2380, (2001).
  2. “An interfacial mechanism inferred from two crystal structures of Mycobacterium tuberculosis 30 kDa major secretory protein (antigen 85B), a mycolyl transferase” Anderson, D.H., Harth, G., Horwitz, M.A. and Eisenberg, D., J. Mol. Biol., 307 (2), 671-681 (2001).
  3. “Mining Literature for Protein-Protein Interactions” Marcotte, E.M., Xenarios, I., and Eisenberg, D. Bioinformatics, 17, 359-363, (2001).
  4. “Three-dimensional Cluster Analysis Identifies Interfaces and Functional Residue Clusters in Proteins” Landgraf, R., Xenarios, I. And Eisenberg, D. J. of Mol. Biol., 307 (5), 1487-1502 (2001).
  5. “The Crystal Structure of a Heptameric Archael Sm Protein: Implications for the Eukaryotic snRNP Core” Mura, C., Cascio, D., Sawaya, M.R. and Eisenberg, D. PNAS USA, 98, 5532-5527. (2001).
  6. “Motif-Based Fold Assignment” Salwinski, L. and Eisenberg, D. Protein Science, 10, 2460-2469 (2001).
  7. “3D Structure and Significance of the GΦXXG Helix Packing Motif in Tetramers of the E1? subunit of the Pyruvate Dehydrogenase from the Archaeon Pyrobaculum Aerophilum” Kleiger, G., Perry, J. and Eisenberg, D. Biochemistry, 40, 14484-14492 (2001).
  8. “Bioinformatic Identification of Potential Autocrine Signaling Loops in Cancers from Gene Expression Profiles”, Graeber, T.G. and Eisenberg, D., Nature Genetics, 29, 295-300 (2001).
  9. “Identification of a Heregulin Binding Site in HER3-ECD by Limited Proteolysis” Singer, E., Landgraf, R., Horan, T., Slamon, D., and Eisenberg, D., J. Biol. Chem., 276, 44266-44274 (2001).
  10. “DIP: The Database of Interacting Proteins. A Research Tool For Studying Cellular Networks Of Protein Interactions” Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., Eisenberg, D., Nucleic Acids Res., 30, 303-305 (2002).
  11. “Structures of Two Three Dimensional Domain-Swapped RNAse A Trimers” Liu, Y., Gotte, G., Libonati, M., and Eisenberg, D., Protein Science, 11, 371-380 (2002).
  12. “Genomic Evidence that the Intracellular Proteins of Archael Microbes Contain Disulfide Bonds.” Mallick, P., Boutz, D. R., Eisenberg, D., and Yeates, T.O., PNAS, 99, 9679-9684 (2002).
  13. “Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit β-sheets” Wang, S., Mura, C., Sawaya, M., Cascio, D., and Eisenberg, D., Acta Cryst. Sect., D58, 571-578 (2002).
  14. “Thiol-Disulfide Exchange in an Immunoglubulin-like Fold: Structure of the N-Terminal Domain of DsbD” Goulding, C.W., Sawaya, M.R., Parseghian, A., Lim, V., Eisenberg, D., Missiakas, D., Biochemistry, 41, 6920-6927 (2002).
  15. “Protein Interactions: Two Methods for assignment of the reliability of high-throughput observations”, Deane, C.M., Salwinski, L., Xenarios, I., Eisenberg, D., Molecular and Cellular Proteomics, 1.5, 349-356 (2002).
  16. “GXXXG and AXXXA: Common α-helical interaction motifs in proteins, particularly in extremeophiles” Kleiger, G., Grothe, R., Mallick, P., and Eisenberg, D., Biochemistry, 41, 5990-5997, (2002).
  17. “Describing biological protein interactions in terms of protein states and state transitions: the Live DIP database” Duan, X.J., Xenarios, I., and Eisenberg, D., Molecular and Cellular Proteomics, 1, 104-116 (2002).
  18. “Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation” Gill, H. S., Pfluegl, G. M. U., Eisenberg, D., Biochemistry, 41, 9863-9872 (2002).
  19. “A Hierarchic Approach to the Design of Hexameric Helical Barrels” Ghirlanda, G., Lear, J.D., Ogihara, N.L., Eisenberg, D., DeGrado, W.F., J. Mol. Biol., 319, 243-253, (2002).
  20. “GXXXG and GXXXA Motifs Stabilize FAD- and NAD(P)- Binding Rossmann Folds Through C Alpha - H…O Hydrogen Bonds and Van Der Waals Interactions” Kleiger, G., Eisenberg, D., J. Mol. Biol., 323, 69-76 (2002).
  21. “Crystal Structure of a Major Secreted Protein of Mycobacterium tuberculosis-MPT63 at 1.5 Angstroms Resolution” Goulding, C., et. al., Protein Science, 11, 2887-2893, (2002).
  22. “The directional atomic solvation energy: An atom-based potential for the assignment of protein sequences to known folds”, Mallick, P., Weiss, R., Eisenberg, D., PNAS, 99, 16041-16046, (2002).
  23. “The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs)”, Mura, C., Kozhukhovsky, a., Gingery, M., Philips, M., Eisenberg, D., Protein Science, 12, 832-847, (2003).
  24. “Granulysin Crystal Structure and a Structure-derived Lytic Mechanism” Anderson, D.H., Sawaya, M. R., Cascio, D., Ernst, W., Modlin, R., Krensky, A., Eisenberg, D., J. Mol. Biol., 325, 355-365, (2003).
  25. “Structure and function of an archaeal homolog of survival protein E (SurEA): An acid phosphatase with a nucleic acid substrate”, Mura, C., Katz, J. E., Clarke, S., Eisenberg, D.,J. Mol. Biol., 326, 1559-1575, (2003).
  26. “Selected Dimerization of a C2H2 Zinc Finger Subfamily” McCarty, A., Kleiger, G., Eisenberg, D., Smale, S. T., Molecular Cell, 11, 459-470, (2003).
  27. “Crystal Structures of a Pantothenate Synthetase from M. tuberculosis and its Complexes with Substrates and a Reaction Intermediate”, Wang, Shuishu, Eisenberg, David, Protein Science, 12, 1097-1108 (2003).
  28. “Inference of protein function and protein linkages in M. tuberculosis based on prokaryotic genome organization: a combined computational approach” Strong, M., Mallick, P., Pellegrini, M., Thompson, M. J., Eisenberg, D., Genome Biology, 4:R59, 2-16, (2003).
  29. “Use of Genetic Profiling in Leprosy to Discriminate Clinical Forms of the Disease” Graeber, T., Li, H.Y., Bleharski, J.R., et. al., Eisenberg, D., Modlin, R. L., Science, 301, 1527-1530 (2003).
  30. “Seeded conversion of recombinant prion protein to a disulfide-bonded oligomer by a reduction-oxidation process”, Sangho Lee and David Eisenberg, Nature Structural Biology, 10, 725-730, (2003).
  31. “Structure and assembly of an augmented Sm-like archaeal protein 14-mer” Mura, C, Phillips, M., Kozhukhovsky, A., Eisenberg D., PNAS, 100, 4539-4544, (2003).
  32. “Visualization and Interpretation of Protein Networks in Mycobacterium tuberculosis Based on Hierarchical Clustering of Genome-Wide Functional Linkage Maps.” Strong, M., Graeber, T. G., Beeby, M., Pellegrini, M., Thompson, M. J., Yeates, T. O., Eisenberg, D., Nucleic Acids Research, 31, 7099-7109, (2003).
  33. “The Primary Mechanism of Attenuation of BCG is a Loss of Secreted Lytic Function Required for Invasion” Hsu, Tsungda et. al., Goulding, C., Gingery, M., Eisenberg, D., Jacobs, W., PNAS, 100, 12420-12425, (2003).
  34. “Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning” Lee, S., Sawaya, M.R., Eisenberg, David, Acta Crystallographica, Section D, D59, 2191- 2199 (2003).
  35. “The Role of the C-Terminal 28 Residues of β-2-Microglobulin in an Amyloid Fibrils Formation” Ivanova, M. I., Ginery, M, Whitson, L. J., and Eisenberg, D. S., Biochemistry, 42, 13536-13540, (2003).
  36. “Use of Genetic Profiling in Leprosy to Discriminate Clinical Forms of the Disease” Bleharski, J. R., LI, H., Meinken, C., Graeber, T., Ochao, M., Yamamura, M., Burdick, A., Sarno, E. N., Wagner, M., Rollinghoff, M., Rea, T. H., Colonna, M., Stenger, S., Bloom, B. R., Eisenberg, D., Modlin, R. L, Science Reprint, 301, 1527-1530, (2003).
  37. “Cross-beta Order and Diversity in Nanocrystals of an Amyloid-forming Peptide”, Ruben Diaz-Avalos, Chris Long, Eric Fontano, Melinda Balbirnie, Robert Grothe, David Eisenberg, and Donald L. D. Caspar, J. Mol. Biol., 330, 1165-1175, (2003).
  38. “The Database of Interacting Proteins: 2004 update” Salwinski, L, Miller, C. S. Smith, A., Pettit, F. K., Bowie, J. U., Eisenberg, D. Nucleic Acids Research, 32, D449-D451, (2004).
  39. “The HUPO PSI's Molecular Interaction Format - A community standard for the representation of protein interaction data” Hermjakob, H. et al. (with Lukasz Salwinski), Nature Biotechnology, 22, 177-183, (2004).
  40. “Gram-positive DsbE proteins function differently from gram-negative DsbE homologs: a structure to function analysis of DsbE from Mycobacterium tuberculosis” Goulding, C., Apostol, M., Gleiter, S., Parseghian, A., Bardwell, J., Gennaro, M., Eisenberg, D., Journal of Biological Chemistry, 279, 3516-3524, (2004).
  41. “PROLINKS: A Database of Protein Functional Linkages Derived from Co-evolution” Bowers, P. M., Pellegrini, M., Thompson, M. J., Fierro, J., Yeates, T. O., Eisenberg, D., Genome Biology, 5:R35.1-R35.13, (2004).
  42. “PFIT and PFRIT: Bioinformatic algorithms for detecting glycosidase function from structure and sequence” Kleiger, G., Panina, E. M., Mallick, P., Eisenberg, D., Protein Science, 13, 221-229, (2004.)
  43. “DPANN: Improved Sequence to Structure Alignments Following Fold-Recognition” Reinhardt, Astrid and Eisenberg, David, PROTEINS: Structure, Function, and Bioinformatics, 56, 528-538, (2004).
  44. “In Silico simulation of biological network dynamics” Lukasz Salwinski and David Eisenberg, Nature Biotechnology, 22, 1017-1019, (2004).
  45. “An amyloid-forming segment of β2-microglobulin suggests a molecular model for the fibril”, Ivanova, M., Sawaya, M. R., Gingery, M., Attinger, A., Eisenberg, D., PNAS, 101, 10584-10589, (2004).
  46. “Use of Logic Relationships to Decipher Protein Network Organization” Peter Bowers, Shawn Cokus, David Eisenberg, Todd Yeates, Science, 306, 2246-2249, (2004).
  47. “Inference of protein function from protein structure”, Debnath Pal and David Eisenberg, Structure, 13, 121-130, (2005).
  48. “Detection of parallel functional modules by comparative analysis of genome sequences” Huiying Li, Matteo Pellegrini, David Eisenberg, Nature Biotechnology, 23, 253-260, (2005).
  49. “The 1.70 Å X-Ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase” Peter Mueller, Michael R. Sawaya, Inna Pashkov, Sum Chan, Chau Nguyen, Yim Wu, L. Jeanne Perry and David Eisenberg, Acta Crystallographica Section D, D61, 309-315, (2005).
  50. “Crystal Structure of a RuBisCO-like Protein from the Green Sulfur Bacterium Chlorobium tepidum” Huiying Li, Michael R. Sawaya, F. Robert Tabita, and David Eisenberg, Structure, 13, 779-789, (2005).
  51. “Regulation by Oligomerization in a Mycobacterial Folate Biosynthetic Enzyme”, Celia Whitford Goulding, Marcin I Apostol, Michael  R Sawaya, Martin Phillips, Angineh Parseghian, David Eisenberg, JMB, 349, 61-72, (2005).
  52. “Structure of the cross-β spine of amyloid-like fibrils” Rebecca Nelson, Michael Sawaya, Melinda Balbirnie, Robert Grothe, Anders Madsen, Christian Riekel, David Eisenberg, Nature, 435, 773-778, (2005).
  53. “Amyloid-like Fibrils of Ribonuclease A with a 3D Domain-Swapped, Native-like Structure”, Shilpa Sambashivan, Yanshun Liu, Michael Sawaya, Mari Gingery, David Eisenberg, Nature, 437, 266-269, (2005).
  54. “Utilizing Logical Relationships in Genomic Data to Decipher Cellular Processes” Peter Bowers, Brian D. O'Connor, Shawn J. Cokus, Einat Sprinzak, Todd O. Yeates, David Eisenberg, FEBS Journal, (European Journal of Biochemistry), FJ-05-0555.R1, 5110-5118, (2005).
  55. “Inferring protein domain interactions from databases of interacting proteins”, Robert Riley, Christopher Lee, Chiara Sabatti, and David Eisenberg, Genome Biology, 6, R89 - R89.17 (2005).
  56. “The 3D Profile Method for Identifying Fibril-Forming Segments of Proteins”, Michael J. Thompson, Stuart A. Sievers, John Karanicolas, Magdalena I. Ivanova, David Baker, and David Eisenberg, PNAS, 103, 4074-4078 (2006).
  57. “A Systematic Screen of β2-Microglobulin and Insulin for Amyloid-Like Segments” Magdalena I. Ivanova, Michael J. Thompson, and David Eisenberg, PNAS, 103, 4079-4082 (2006).
  58. “Bioinformatic Challenges for the Next Decade(s)” David Eisenberg, Edward Marcotte, Anderew D. McLachlan, Matteo Pellegrini, Philos Trans R Soc Lond B Biol Sci. Mar 29;361(1467):525-7, (2006).
  59. “Mycobacterium tuberculosis gene expression profiling within the context of protein networks” Helmy Rachman, Michael Strong, Ulrich Schaible, Johannees Schuchhardt, Kristine Hagens, Hans Mollenkopf, David Eisenberg, Stefan H. E. Kaufmann, Microbes and Infection xx, 1-11, (2006).
  60. “Unique Transcriptome Signature of Mycobacterium tuberculosis in Pulmonary Tuberculosis” Helmy Rachman, Michael Strong, Timo Ulrichs, Leander Grode, Johannes Schuchhardt, Hans Mollenkopf, George A. Kosmiadi, David Eisenberg, and Stefan H.E. Kaufmann, Infection and Immunity, 74.2, 1233-1242, (2006).
  61. “Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I” Zhefeng Guo and David Eisenberg, PNAS, 103, 8042-8047, (2006).
  62. “Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis” Michael Strong, Michael R. Sawaya, Shuishu Wang, Martin Phillips, Duilio Cascio, David Eisenberg, PNAS,103, 8060-8065, (2006).
  63. “Toll-Like Receptor Triggering of a Vitamin D-Mediated Human Antimicrobial Response” Philip T. Liu, Steffen Stenger, Huiying Li, Linda Wenzel, Belinda H. Tan, Stephan R. Krutzik, Maria Teresa Ochao, Jurgen Schauber, Kent Wu, Christoph Meinken, Diane L. Kamen, Manfred Wagner, Robert Bals, Andreas Steinmeyer, Ulrich Zugel, Richard L. Gallo, David Eisenberg, Martin Hewison, Bruce W. Hollis, John S. Adams, Barry R. Bloom, Robert L. Modlin, Science, 311, 1770-1773, (2006).
  64. “Cooperative Hydrogen-Bonding in Amyloid Formation” Kiril Tsemekhman, Lukasz Goldschmidt, David Eisenberg, David Baker, Protein Science, 16:1-4, (2007).
  65. “A Novel Inhibitor of Mycobacterium tuberculosis Pantothenate Synthetase” E. Lucile White, Kristen Southworth, Larry Ross, Sara Cooley, Rachel B. Gill, Melinda Ingrum Sosa, Anna Manouvakhova, Lynn Rasmussen, Celia Goulding, David Eisenberg, and Thomas M. Fletcher III, Journal of Biomolecular Screening 12(1); 100-105, (2007).