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Director,
UCLA-DOE Institute for Genomics & Proteomics
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Distinguished Professor,
Biological Chemistry
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Professor,
Chemistry and Biochemistry
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Member,
ACCESS Program: Dept. of Biological Chemistry,
California NanoSystems Institute,
JCCC Cancer Cell Biology Program Area
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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 a Professor of Chemistry & Biochemistry, as well as the Director of the DOE Lab of Structural Biology & Molecular Medicines at UCLA. Before he assumed his role in the UCLA community Mr. Eisenberg received an A.B. in Biochemical Science from Harvard College and preceded to Oxford University where he completed his D.Phil. in Theoretical Chemistry. After completing two Postdoctorales, one at Princeton University regarding water and hydrogen bonding and the other at the California Institute of Technology on protein crystallography, he joined the faculty at UCLA. Currently his research involves the use of x-ray crystallography and the long-term goal of understanding and manipulating the metabolism of cells through the interactions of their constituent proteins. Throughout his career Mr. Eisenberg has published over 200 papers, holds several patents and has presented over 10 lectureships through the University of Michigan, Purdue, Harvard to name a few. Of his many awards some highlights include; Alfred P. Sloan Fellow, UCLA Distinguished Teaching Award, John Simon Guggenheim Fellow, UCLA Faculty Research Lectureship, National Academy of Sciences Member, American Academy of Arts and Sciences Member.
Publications:
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.
Medrano-Soto, A. Pal, D. Eisenberg, D. Inferring molecular function: contributions from functional linkages.
Trends Genet.
2008; 24( 12):
587-90.
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.
Sawaya, MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL A Double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms.
Cell
2008; 134(6):
1007-18.
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.
Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R Bacterial Inclusion Bodies Contain Amyloid-Like Structure.
PLoS Biol
2008; 6(8):
.
Miallau, L., Faller, M., Chiang, J., Arbing, M., Guo, F., Cascio, D., Eisenberg, D. Structure and Proposed Activity of a Member of the VAPBC Family og Toxin-Antitoxin Systems: VAPBC-5 from Mycobacterium Tuberculosis.
J. Biol. Chem.
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):
.
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.
Tsemekhman, K. Goldschmidt, L. Eisenberg, D. Baker, D. Cooperative hydrogen bonding in amyloid formation.
Protein Sci.
2007; 16( 4):
761-4.
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.
Strong, M. Eisenberg, D. The protein network as a tool for finding novel drug targets.
Prog Drug Res.
2007; 64(number):
191, 193-215.
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.
Nelson, R. Eisenberg, D. Recent atomic models of amyloid fibril structure.
Curr Opin Struct Biol.
2006; 16( 2):
260-5.
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.
Li, H. Pellegrini, M. Eisenberg, D. Detection of parallel functional modules by comparative analysis of genome sequences.
Nat Biotechnol.
2005; 23( 2):
253-60.
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.
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. 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.
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.
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.
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.
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.
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.
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.
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;
.
Miller Christopher S, Eisenberg David Using inferred residue contacts to distinguish between correct and incorrect protein models..
Bioinformatics.
2008; 24(14):
1575-82.
Kuriyan John, Eisenberg David The origin of protein interactions and allostery in colocalization..
Nature.
2007; 450(7172):
983-90.
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.
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.
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.
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.
Sawaya, M. R. Sambashivan, S. Nelson, R. Ivanova, M. I. Sievers, S. A. Apostol, M. I. Thompson, M. J. Balbirnie, M. Wiltzius, J. J. McFarlane, H. T. Madsen, A. O. Riekel, C. Eisenberg, D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Nature.
2007; 447( 7143):
453-7.
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.
Guo Zhefeng, Eisenberg David The mechanism of the amyloidogenic conversion of T7 endonuclease I..
J. Biol. Chem..
2007; 282(20):
14968-74.
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.
Eisenberg David, Nelson Rebecca, Sawaya Michael R, Balbirnie Melinda, Sambashivan Shilpa, Ivanova Magdalena I, Madsen Anders Ã, Riekel Christian The structural biology of protein aggregation diseases: Fundamental questions and some answers..
Acc. Chem. Res..
2006; 39(9):
568-75.
Bennett Melanie J, Sawaya Michael R, Eisenberg David Deposition diseases and 3D domain swapping..
Structure.
2006; 14(5):
811-24.
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.
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.
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.
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.
Nelson Rebecca, Eisenberg David Structural models of amyloid-like fibrils..
Adv. Protein Chem..
2006; 73(2):
235-82.
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.
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. Cokus, S. J. Eisenberg, D. Yeates, T. O. Use of logic relationships to decipher protein network organization.
Science.
2004; 306( 5705):
2246-9.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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. 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. 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.
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