UCLA Department of Biological Chemistry

David S. Eisenberg, Ph.D.

Work Email Address:
david@mbi.ucla.edu Laboratory Address:
Paul Boyer Hall 205

UNITED STATES

Mailing Address:
201A Paul Boyer Hall
CAMPUS - 157005
Los Angeles, CA

Work Address:
Paul Boyer Hall 201A

Fax Number:
(310) 206-3914
Lab Number:
1 (310) 206-3642
Work Phone Number:
1 (310) 825-3754

Web Address:
David Eisenberg's Website
Web Address:
David Eisenberg's Website

David S. Eisenberg, Ph.D.

Department / Division Affiliations
Paul D. Boyer Professor of Molecular Biology & Biochemistry, Molecular Biology Institute
Distinguished Professor, Biological Chemistry
Professor, Chemistry and Biochemistry
Director, UCLA-DOE Institute for Genomics & Proteomics
Lab Director, Eisenberg Lab
ACCESS Affinity Group:
ACCESS Affinity - Structural Biology & Proteomics

Awards and Honors:

UCLA McCoy Award
Amgen Award of the Protein Society
Pierce Award of the Immunotoxin Society
Biophysical Society Emily M. Gray Award, 2008
Technion - Israel Institute of Technology Harvey Prize in Human Health, 2008
Preceptor for the 2009 Nobel Laureate Signature Award for Graduate Education in Chemistry, 2008
Harvard Westheimer Medal, 2005
UCLA Seaborg Medal, 2004
Howard Hughes Medical Institute Investigator, 2001
National Academy of Sciences Elected Member, 1989
American Association for the Advancement of Science Fellow
American Philosophical Society Member
Institute of Medicine Member

Research Interest:

Protein Structure, Folding, and Design
David Eisenberg focuses on protein interactions. In his experiments he studies the structural basis for conversion of normal proteins to the amyloid state and conversion of prions to the infectious state. In bioinformatic work, he derives information on protein interactions from genomic and proteomic data. His goal is to learn the networks of interacting proteins in cells.

Biography:

David Eisenberg is currently Professor of Chemistry and Biochemistry and Biological Chemistry, as well as HHMI Investigator and Director of the UCLA-DOE Institute for Genomics and Proteomics. Before he came to UCLA, Eisenberg earned an A.B. in Biochemical Sciences from Harvard College and a D.Phil. from Oxford University in Theoretical Chemistry on a Rhodes Scholarship. After postdoctoral study at Princeton University on water and hydrogen bonding and at Caltech on protein crystallography, he joined the faculty at UCLA. Currently he studies protein interactions by X-ray crystallography, bioinformatics, and biochemistry, with an emphasis on amyloid-forming proteins. This recently recognized protein state offers opportunities to understand cells in health and disease, and in synthesizing new materials and in understanding processes as diverse as biofilms and corrosion. Eisenberg has published over 300 papers and reviews, holds half a dozen patents. His awards include: the UCLA Distinguished Teaching Award, John Simon Guggenheim Fellowship, the UCLA Faculty Research Lectureship, the Stein and Moore Award of the Protein Society, the ACS Faculty Mentoring Award, and membership in the National Academy of Sciences, the American Academy of Arts and Sciences, the American Philosophical Society, and the Institute of Medicine.

Publications:

Goldschmidt Lukasz, Teng Poh K, Riek Roland, Eisenberg David Identifying the amylome, proteins capable of forming amyloid-like fibrils.. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107(8): 3487-92.

Wang Lei, Schubert David, Sawaya Michael R, Eisenberg David, Riek Roland Multidimensional Structure-Activity Relationship of a Protein in Its Aggregated States.. Angewandte Chemie. 2010; 49(23): 3904-8.

Eisenberg David L, Stika Catherine, Desai Ami, Baker David, Yost Kathleen J Providing contraception for women taking potentially teratogenic medications: a survey of internal medicine physicians' knowledge, attitudes and barriers.. Journal of general internal medicine. 2010; 25(4): 291-7.

Wiltzius JJ, Sievers SA, Sawaya MR, Eisenberg D Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process. Protein Science. 2009; 18(7): 1521-30.

Sprinzak Einat, Cokus Shawn J, Yeates Todd O, Eisenberg David, Pellegrini Matteo Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.. BMC systems biology. 2009; 3(1): 115.

Maji Samir K, Perrin Marilyn H, Sawaya Michael R, Jessberger Sebastian, Vadodaria Krishna, Rissman Robert A, Singru Praful S, Nilsson K Peter R, Simon Rozalyn, Schubert David, Eisenberg David, Rivier Jean, Sawchenko Paul, Vale Wylie, Riek Roland Functional amyloids as natural storage of peptide hormones in pituitary secretory granules.. Science (New York, N.Y.). 2009; 325(5938): 328-32.

Ivanova Magdalena I, Sievers Stuart A, Sawaya Michael R, Wall Joseph S, Eisenberg David Molecular basis for insulin fibril assembly.. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106(45): 18990-5.

Wiltzius Jed J W, Landau Meytal, Nelson Rebecca, Sawaya Michael R, Apostol Marcin I, Goldschmidt Lukasz, Soriaga Angela B, Cascio Duilio, Rajashankar Kanagalaghatta, Eisenberg David Molecular mechanisms for protein-encoded inheritance.. Nature structural & molecular biology. 2009; 16(9): 973-8.

Salwinski Lukasz, Licata Luana, Winter Andrew, Thorneycroft David, Khadake Jyoti, Ceol Arnaud, Aryamontri Andrew Chatr, Oughtred Rose, Livstone Michael, Boucher Lorrie, Botstein David, Dolinski Kara, Berardini Tanya, Huala Eva, Tyers Mike, Eisenberg David, Cesareni Gianni, Hermjakob Henning Recurated protein interaction datasets.. Nature methods. 2009; 6(12): 860-1.

Teng Poh K, Eisenberg David Short protein segments can drive a non-fibrillizing protein into the amyloid state.. Protein engineering, design & selection : PEDS. 2009; 22(8): 531-6.

Miallau Linda, Faller Michael, Chiang Janet, Arbing Mark, Guo Feng, Cascio Duilio, Eisenberg David Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis.. The Journal of biological chemistry. 2009; 284(1): 276-83.

Sawaya, M. R. Wojtowicz, W. M. Andre, I. Qian, B. Wu, W. Baker, D. Eisenberg, D. Zipursky, S. L. A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell. 2008; 134(6): 1007-18.

Llewellyn Richard, Eisenberg David S Annotating proteins with generalized functional linkages.. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(46): 17700-5.

Wiltzius JJ, Sievers SA, Sawaya MR, Cascio D, Popov D, Riekel C, Eisenberg D Atomic Structure of the Cross-Beta Spine of Islet Amyloid Polypeptide. Protein Science. 2008; 17(9): 1467-74.

Wiltzius Jed J W, Sievers Stuart A, Sawaya Michael R, Cascio Duilio, Popov Dmitriy, Riekel Christian, Eisenberg David Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin). Protein science : a publication of the Protein Society. 2008; 17(9): 1467-74.

Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R Bacterial Inclusion Bodies Contain Amyloid-Like Structure. PLoS Biol. 2008; 6(8): .

Zhang Kechun, Sawaya Michael R, Eisenberg David S, Liao James C Expanding metabolism for biosynthesis of nonnatural alcohols.. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(52): 20653-8.

Cruz, D. Watson, A. D. Miller, C. S. Montoya, D. Ochoa, M. T. Sieling, P. A. Gutierrez, M. A. Navab, M. Reddy, S. T. Witztum, J. L. Fogelman, A. M. Rea, T. H. Eisenberg, D. Berliner, J. Modlin, R. L. Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy. J Clin Invest. 2008; 118(8): 2917-28.

Cruz, Watson, Miller, Montoya, Ochoa, Sieling, Gutierrez, Navab, Reddy, Witztum, Fogelman, Rea, Eisenberg, Berliner, Modlin Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy.. J. Clin. Invest.. 2008; .

Riley, R., Pellegrini, M., Eisenberg, D. Identifying Cognate Binding Pairs Among a Large set of Paralogs: the Case of PE/PPE Proteins of Mycobacterium Tuberculosis. PLoS Comput. Biol.. 2008; 4(9): .

Medrano-Soto, A. Pal, D. Eisenberg, D. Inferring molecular function: contributions from functional linkages. Trends Genet. 2008; 24(12): 587-90.

Dunn B., Long J.W., Rolison D.R. Rethinking Multifunctions in Three Dimensions for Miniaturizing Electrical Energy Storage. Interface. 2008; 17(3): 49.

Guo, Z. Eisenberg, D. The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold. Protein Sci. 2008; 17(9): 1617-23.

Miller Christopher S, Eisenberg David Using inferred residue contacts to distinguish between correct and incorrect protein models.. Bioinformatics. 2008; 24(14): 1575-82.

White, E. L. Southworth, K. Ross, L. Cooley, S. Gill, R. B. Sosa, M. I. Manouvakhova, A. Rasmussen, L. Goulding, C. Eisenberg, D. Fletcher, T. M., 3rd A novel inhibitor of Mycobacterium tuberculosis pantothenate synthetase. J Biomol Screen. 2007; 12(1): 100-5.

Sawaya Michael R, Sambashivan Shilpa, Nelson Rebecca, Ivanova Magdalena I, Sievers Stuart A, Apostol Marcin I, Thompson Michael J, Balbirnie Melinda, Wiltzius Jed J W, McFarlane Heather T, Madsen Anders Ã, Riekel Christian, Eisenberg David Atomic structures of amyloid cross-beta spines reveal varied steric zippers.. Nature. 2007; 447(7143): 453-7.

Galynker,, II Eisenberg, D. Matochik, J. A. Gertmenian-King, E. Cohen, L. Kimes, A. S. Contoreggi, C. Kurian, V. Ernst, M. Rosenthal, R. N. Prosser, J. London, E. D. Cerebral metabolism and mood in remitted opiate dependence. Drug Alcohol Depend. 2007; 90(2-3): 166-74.

Tsemekhman, K. Goldschmidt, L. Eisenberg, D. Baker, D. Cooperative hydrogen bonding in amyloid formation. Protein Sci. 2007; 16(4): 761-4.

Anderson Daniel H, Kickhoefer Valerie A, Sievers Stuart A, Rome Leonard H, Eisenberg David Draft crystal structure of the vault shell at 9-A resolution.. PLoS Biol.. 2007; 5(11): e318.

Anderson, D. H. Kickhoefer, V. A. Sievers, S. A. Rome, L. H. Eisenberg, D. Draft crystal structure of the vault shell at 9-A resolution. PLoS Biol. 2007; 5(11): e318.

Kim Sul-Min, Bowers Peter M, Pal Debnath, Strong Michael, Terwilliger Thomas C, Kaufmann Markus, Eisenberg David Functional linkages can reveal protein complexes for structure determination.. Structure. 2007; 15(9): 1079-89.

Salwinski Lukasz, Eisenberg David The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.. Bioinformatics. 2007; 23(16): 2193-5.

Guo Zhefeng, Eisenberg David The mechanism of the amyloidogenic conversion of T7 endonuclease I.. J. Biol. Chem.. 2007; 282(20): 14968-74.

Kuriyan John, Eisenberg David The origin of protein interactions and allostery in colocalization.. Nature. 2007; 450(7172): 983-90.

Strong, M. Eisenberg, D. The protein network as a tool for finding novel drug targets. Prog Drug Res. 2007; 64(number): 191, 193-215.

Strong Michael, Eisenberg David The protein network as a tool for finding novel drug targets.. Mol. Ther.. 2007; 64(1): 191, 193-215.

Goulding Celia W, Bowers Peter M, Segelke Brent, Lekin Tim, Kim Chang-Yub, Terwilliger Thomas C, Eisenberg David The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function.. J. Mol. Biol.. 2007; 365(2): 275-83.

Goldschmidt, L. Cooper, D. R. Derewenda, Z. S. Eisenberg, D. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Protein Sci. 2007; 16(8): 1569-76.

Goldschmidt Lukasz, Cooper David R, Derewenda Zygmunt S, Eisenberg David Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.. Protein Sci.. 2007; 16(8): 1569-76.

Ivanova, M. I. Thompson, M. J. Eisenberg, D. A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments. Proc Natl Acad Sci U S A. 2006; 103(11): 4079-82.

Eisenberg, D. Marcotte, E. McLachlan, A. D. Pellegrini, M. Bioinformatic challenges for the next decade(s). Philos Trans R Soc Lond B Biol Sci. 2006; 361(1467): 525-7.

Bennett Melanie J, Sawaya Michael R, Eisenberg David Deposition diseases and 3D domain swapping.. Structure. 2006; 14(5): 811-24.

Nelson, R. Eisenberg, D. Recent atomic models of amyloid fibril structure. Curr Opin Struct Biol. 2006; 16(2): 260-5.

Guo Zhefeng, Eisenberg David Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I.. Proc. Natl. Acad. Sci. U.S.A.. 2006; 103(21): 8042-7.

Nelson Rebecca, Eisenberg David Structural models of amyloid-like fibrils.. Adv. Protein Chem.. 2006; 73(2): 235-82.

Thompson, M. J. Sievers, S. A. Karanicolas, J. Ivanova, M. I. Baker, D. Eisenberg, D. The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci U S A. 2006; 103(11): 4074-8.

Eisenberg, D. Nelson, R. Sawaya, M. R. Balbirnie, M. Sambashivan, S. Ivanova, M. I. Madsen, A. O. Riekel, C. The structural biology of protein aggregation diseases: Fundamental questions and some answers. Acc Chem Res. 2006; 39(9): 568-75.

Strong Michael, Sawaya Michael R, Wang Shuishu, Phillips Martin, Cascio Duilio, Eisenberg David Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.. Proc. Natl. Acad. Sci. U.S.A.. 2006; 103(21): 8060-5.

Sambashivan, S. Liu, Y. Sawaya, M. R. Gingery, M. Eisenberg, D. Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Nature. 2005; 437(7056): 266-9.

Li, H. Pellegrini, M. Eisenberg, D. Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol. 2005; 23(2): 253-60.

Nelson, R. Sawaya, M. R. Balbirnie, M. Madsen, A. O. Riekel, C. Grothe, R. Eisenberg, D. Structure of the cross-beta spine of amyloid-like fibrils. Nature. 2005; 435(7043): 773-8.

Bowers, P. M. O'Connor, B. D. Cokus, S. J. Sprinzak, E. Yeates, T. O. Eisenberg, D. Utilizing logical relationships in genomic data to decipher cellular processes. FEBS J. 2005; 272(20): 5110-8.

Ivanova, M. I. Sawaya, M. R. Gingery, M. Attinger, A. Eisenberg, D. An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril. Proc Natl Acad Sci U S A. 2004; 101(29): 10584-9.

Goulding, C. W. Apostol, M. I. Gleiter, S. Parseghian, A. Bardwell, J. Gennaro, M. Eisenberg, D. Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis. J Biol Chem. 2004; 279(5): 3516-24.

Kleiger, G. Panina, E. M. Mallick, P. Eisenberg, D. PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence. Protein Sci. 2004; 13(1): 221-9.

Salwinski, L. Miller, C. S. Smith, A. J. Pettit, F. K. Bowie, J. U. Eisenberg, D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004; 32(Database issue): D449-51.

Bowers, P. M. Cokus, S. J. Eisenberg, D. Yeates, T. O. Use of logic relationships to decipher protein network organization. Science. 2004; 306(5705): 2246-9.

Salwinski, L. Eisenberg, D. Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol. 2003; 13(3): 377-82.

Wang, S. Eisenberg, D. Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate. Protein Sci. 2003; 12(5): 1097-108.

Anderson, D. H. Sawaya, M. R. Cascio, D. Ernst, W. Modlin, R. Krensky, A. Eisenberg, D. Granulysin crystal structure and a structure-derived lytic mechanism. J Mol Biol. 2003; 325(2): 355-65.

Strong, M. Mallick, P. Pellegrini, M. Thompson, M. J. Eisenberg, D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol. 2003; 4(9): R59.

Ivanova, M. I. Gingery, M. Whitson, L. J. Eisenberg, D. Role of the C-terminal 28 residues of beta2-microglobulin in amyloid fibril formation. Biochemistry. 2003; 42(46): 13536-40.

Lee, S. Eisenberg, D. Seeded conversion of recombinant prion protein to a disulfide-bonded oligomer by a reduction-oxidation process. Nat Struct Biol. 2003; 10(9): 725-30.

McCarty, A. S. Kleiger, G. Eisenberg, D. Smale, S. T. Selective dimerization of a C2H2 zinc finger subfamily. Mol Cell. 2003; 11(2): 459-70.

Cech, T. R. Eddy, S. R. Eisenberg, D. Hersey, K. Holtzman, S. H. Poste, G. H. Raikhel, N. V. Scheller, R. H. Singer, D. B. Waltham, M. C. Sharing publication-related data and materials: responsibilities of authorship in the life sciences. Plant Physiol. 2003; 132(1): 19-24.

Mura, C. Phillips, M. Kozhukhovsky, A. Eisenberg, D. Structure and assembly of an augmented Sm-like archaeal protein 14-mer. Proc Natl Acad Sci U S A. 2003; 100(8): 4539-44.

Mura, C. Katz, J. E. Clarke, S. G. Eisenberg, D. Structure and function of an archaeal homolog of survival protein E (SurEalpha): an acid phosphatase with purine nucleotide specificity. J Mol Biol. 2003; 326(5): 1559-75.

Eisenberg, D. The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins. Proc Natl Acad Sci U S A. 2003; 100(20): 11207-10.

Hsu, T. Hingley-Wilson, S. M. Chen, B. Chen, M. Dai, A. Z. Morin, P. M. Marks, C. B. Padiyar, J. Goulding, C. Gingery, M. Eisenberg, D. Russell, R. G. Derrick, S. C. Collins, F. M. Morris, S. L. King, C. H. Jacobs, W. R., Jr. The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue. Proc Natl Acad Sci U S A. 2003; 100(21): 12420-5.

Strong, M. Graeber, T. G. Beeby, M. Pellegrini, M. Thompson, M. J. Yeates, T. O. Eisenberg, D. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003; 31(24): 7099-109.

Liu, Y. Eisenberg, D. 3D domain swapping: as domains continue to swap. Protein Sci. 2002; 11(6): 1285-99.

Duan, X. J. Xenarios, I. Eisenberg, D. Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database. Mol Cell Proteomics. 2002; 1(2): 104-16.

Kleiger, G. Grothe, R. Mallick, P. Eisenberg, D. GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles. Biochemistry. 2002; 41(19): 5990-7.

Kleiger, G. Eisenberg, D. GXXXG and GXXXA motifs stabilize FAD and NAD(P)-binding Rossmann folds through C(alpha)-H... O hydrogen bonds and van der waals interactions. J Mol Biol. 2002; 323(1): 69-76.

Deane, C. M. Salwinski, L. Xenarios, I. Eisenberg, D. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics. 2002; 1(5): 349-56.

Liu, Y. Gotte, G. Libonati, M. Eisenberg, D. Structures of the two 3D domain-swapped RNase A trimers. Protein Sci. 2002; 11(2): 371-80.

Mallick, P. Weiss, R. Eisenberg, D. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc Natl Acad Sci U S A. 2002; 99(25): 16041-6.

Goulding, C. W. Sawaya, M. R. Parseghian, A. Lim, V. Eisenberg, D. Missiakas, D. Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD. Biochemistry. 2002; 41(22): 6920-7.

Kleiger, G. Perry, J. Eisenberg, D. 3D structure and significance of the GPhiXXG helix packing motif in tetramers of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum. Biochemistry. 2001; 40(48): 14484-92.

Graeber, T. G. Eisenberg, D. Bioinformatic identification of potential autocrine signaling loops in cancers from gene expression profiles. Nat Genet. 2001; 29(3): 295-300.

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