UCLA Chemistry and Biochemistry
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David Eisenberg, Ph.D.

Website:

David Eisenberg's Home Page.

Work Email Address:

david@mbi.ucla.edu

Mailing Address:

201 Paul Boyer Hall
CAMPUS - 157005
Los Angeles, CA

Office Address:

Paul Boyer Hall 201A

Lab Number:

1 (310) 206-3642

Work Phone Number:

1 (310) 825-3754
Professor
Chemistry and Biochemistry, Biochemistry
Distinguished Professor
Biological Chemistry
Member
ACCESS Program: Dept. of Biological Chemistry, California NanoSystems Institute, JCCC Cancer Cell Biology Program Area

A Short Biography:

David Eisenberg is also Professor of Chemistry and Biochemistry and of Biological Chemistry at the University of California, Los Angeles, and Director of the UCLA-DOE Institute for Genomics and Proteomics. He received his undergraduate degree in biochemical sciences from Harvard College and his D.Phil. degree in theoretical chemistry from Oxford University. His postdoctoral research was on ice and water with Walter Kauzmann at Princeton and in protein crystallography with Richard Dickerson. Dr. Eisenberg is a member of the National Academy of Sciences and the Institute of Medicine. He is a recipient of the 2004 UCLA Seaborg Medal, the 2005 Harvard Westheimer Medal, and the 2008 Emily Gray Award from the Biophysical Society.

Awards and Honors:

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

Research Interest:

Protein interactions are studied by X-ray crystallography, and computational and biochemical methods. The long term goal is to understand and manipulate the metabolism of cells through the interactions of their constituent proteins.

One goal is to be able to infer functional linkages of proteins, on the basis of genome sequences and protein expression data. Computational methods have been developed for establishing these relationships, including the phylogenetic profile and Rosetta Stone methods. To benchmark these computational methods, a large Database of Interacting Proteins has been built up.

X-ray crystallography remains a powerful tool for exploring protein structure and interactions. Our X-ray projects are of two types. The first are on amyloids and prions, pathologically interacting proteins. The goal is to understand the structures that underlie the pathologies. The other projects are on the structural biology of Mycobacterium tuberculosis, as part of the TB Structural Genomics Consortium.


Detailed 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.
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.
Wiltzius, Sievers, Sawaya, Eisenberg   Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process. Protein science : a publication of the Protein Society, 2009; .
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.
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.
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.
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 Ø, 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 Ø, 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.
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.
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.
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.
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.
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