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David Eisenberg, Ph.D.

   
Distinguished Professor, Biological Chemistry
Lab Director, Eisenberg Lab
Professor, Chemistry and Biochemistry, Biochemistry, Molecular Biology
Paul D. Boyer Professor of Molecular Biology & Biochemistry, Molecular Biology Institute
Member, Biochemistry, Biophysics & Structural Biology GPB Home Area, Bioinformatics GPB Home Area, CTSI, California NanoSystems Institute, JCCC Signal Transduction and Therapeutics Program Area, Molecular Biology Institute, Molecular Pharmacology GPB Home Area
Researcher, Biochemistry, Biophysics and Structural Biology, Proteomics and Bioinformatics
Investigator, Howard Hughes Medical Institute

Education:
Degrees:
Ph.D., Oxford University, 1961 - 1964
A.B., Harvard College, 1957 - 1961
M.A., Cambridge, 1961 -

Academic Experience:
Fellowships:
2010 - Queen’s College, Oxford, Honorary Fellow
1999 - Biophysical Society, Inaugural Fellow
1991 - American Academy of Arts and Sciences, Fellow
1985 - Guggenheim Memorial Foundation, Guggenheim Fellowship
1969 - Alfred P. Sloan Foundation, Alfred P. Sloan Fellowship
1966 - 1969 California Institute of Technology, Postdoc, Chemistry
1964 - Princeton University, Postdoc, Chemistry
Lecturer:
1989 - UCLA Faculty Research Lectureship

Honors and Awards:
2013 - International Society for Computational Biology, ISCB Award
2009 - Biophysical Society, Emily Gray Award
2009 - Amer Chemical Society, Preceptor for the Nobel Laureate Signature Award
2009 - Technion - Israel Institute of Technology, Harvey Prize in Human Health
2008 - Biophysical Society, Emily M. Gray Award (with Donald Crothers)
2005 - Harvard, Westheimer Medal
2004 - UCLA, Seaborg Medal
2001 - Howard Hughes Medical Institute, Investigator
2000 - The Protein Society, Amgen Award
1998 - Amer Chemical Society, Repligen Award in Molecular Biology
1997 - Biophysical Society, National Lecture Award
1997 - African-American Male Achiever Network, Honoree
1996 - Protein Society, Stein & Moore Award
1992 - The Immunotoxin Society, Pierce Award
1989 - National Academy of Sciences, Elected Member
1982 - UCLA, McCoy Award
1975 - UCLA Distinguished Teaching Award
1972 - U.S. Public Health Service, USPHS Career Development Award
1961 - Oxford University, Rhodes Scholarship
1961 - Harvard University, L.J. Henderson Prize
1958 - 1960 Harvard Scholarship, Honorary Scholarships: Phi Beta Kappa; Sigma Xi

Professional Societies:
2003 - American Philosophical Society, Member
2002 - Institute of Medicine, Member
2001 - American Association for the Advancement of Science, Fellow

Contact Information:
Work Email Address: david@mbi.ucla.edu
Office Address: Howard Hughes Medical Institute
University of California, Los Angeles
611 C.E. Young Drive East
Los Angeles, CA 90095
UNITED STATES
Home Page: http://www.doe-mbi.ucla.edu/People/Eisenberg/
Fax Number: (310) 206-3914 Fax
Office Phone Number: (310) 825-3754 Office
Research Interests:

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.




Technical Research Interest:

Protein Structure, Folding, and Design

The questions explored in our research are described roughly by the current buzz words structural genomics and bioinformatics. Protein structures are determined by x-ray crystallography, and structures are related to function by biochemical, computational and genetic methods. Excellent facilities for structure determination and computation are shared with other members of the UCLA-DOE Lab of Structural Biology and Molecular Medicine.




Additional Information:

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.

Selected Scientific Public Service
    • 2009-2015 SAB St. Jude Children’s Research Hospital
    • 2008-2009 Pfizer’s Biotherapeutics and Bioinnovation Scientific Advisory Panel
    • 2007-2017 SAB UCSF HARC Center
    • 2006-2009 SAB, BioDesign Institute, Arizona State University
    • 2005-2012 SAB, Harvard University Bauer Center
    • 2001-2012 Advisory Committee, Caltech Beckman Center
    • 2004 Review Panel: Centre for Protein Engineering, LMB, Cambridge, UK
    • 2001-2004 National Academy of Sciences: Organizing Chair, Biophysics Section
    • 1999-2005 European Molecular Biology Organization (EMBL) Scientific Advisory Committee
    • 1998-2001 National Research Council, Commission on Life Sciences
    • 1996-2000 Hereditary Disease Foundation, Scientific Advisory Board
    • 1995-1998 National Research Council, Board of Biology
    • 1995-1999 Chair, Protein Data Bank Advisory Board
    • 1989-present Editorial Advisory Board, Current Opinion in Biology
    • 1988-2009 Editor, Advances in Protein Chemistry
    • 1987-1989 First President, Protein Society


Selected Publications:

Miallau Linda, Jain Paras, Arbing Mark A, Cascio Duilio, Phan Tung, Ahn Christine J, Chan Sum, Chernishof Irina, Maxson Michelle, Chiang Janet, Jacobs William R, Eisenberg David S, Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes, Structure (London, England : 1993), 2013, 21 (4), 627-37.
Cheng Pin-Nan, Liu Cong, Zhao Minglei, Eisenberg David, Nowick James S, Amyloid β-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity, Nature chemistry, 2012, 4 (11), 927-33.
Laganowsky Arthur, Liu Cong, Sawaya Michael R, Whitelegge Julian P, Park Jiyong, Zhao Minglei, Pensalfini Anna, Soriaga Angela B, Landau Meytal, Teng Poh K, Cascio Duilio, Glabe Charles, Eisenberg David, Atomic view of a toxic amyloid small oligomer, Science (New York, N.Y.), 2012, 335 (6073), 1228-31.
Kato Masato, Han Tina W, Xie Shanhai, Shi Kevin, Du Xinlin, Wu Leeju C, Mirzaei Hamid, Goldsmith Elizabeth J, Longgood Jamie, Pei Jimin, Grishin Nick V, Frantz Douglas E, Schneider Jay W, Chen She, Li Lin, Sawaya Michael R, Eisenberg David, Tycko Robert, McKnight Steven L, Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels, Cell, 2012, 149 (4), 753-67.
Liu Cong, Zhao Minglei, Jiang Lin, Cheng Pin-Nan, Park Jiyong, Sawaya Michael R, Pensalfini Anna, Gou Dawei, Berk Arnold J, Glabe Charles G, Nowick James, Eisenberg David, Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates, Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (51), 20913-8.
Teng Poh K, Anderson Natalie J, Goldschmidt Lukasz, Sawaya Michael R, Sambashivan Shilpa, Eisenberg David, Ribonuclease A suggests how proteins self-chaperone against amyloid fiber formation, Protein science : a publication of the Protein Society, 2012, 21 (1), 26-37.
Eisenberg David, Jucker Mathias, The amyloid state of proteins in human diseases, Cell, 2012, 148 (6), 1188-203.
Min Andrew B, Miallau Linda, Sawaya Michael R, Habel Jeff, Cascio Duilio, Eisenberg David, 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, Protein science : a publication of the Protein Society, 2012, 21 (11), 1754-67.
Stroud James C, Liu Cong, Teng Poh K, Eisenberg David, Toxic fibrillar oligomers of amyloid-β have cross-β structure, Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (20), 7717-22.
Cong Liu, Michael R Sawaya & David Eisenberg, ?2-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages, Nature Structural & Molecular Biology, 2011, 18, 49-55.
Apostol MI, Wiltzius JJ, Sawaya MR, Cascio D, Eisenberg D, Atomic structures suggest determinants of transmission barriers in Mammalian prion disease, Biochemistry, 2011, 50 (13), 2456-63.
Apostol Marcin I, Wiltzius Jed J W, Sawaya Michael R, Cascio Duilio, Eisenberg David, Atomic structures suggest determinants of transmission barriers in mammalian prion disease, Biochemistry, 2011, 50 (13), 2456-63.
Liu Cong, Sawaya Michael R, Cheng Pin-Nan, Zheng Jing, Nowick James S, Eisenberg David, Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic β-sheet mimics, Journal of the American Chemical Society, 2011, 133 (17), 6736-44.
Zheng J, Liu C, Sawaya MR, Vadla B, Khan S, Woods RJ, Eisenberg D, Goux WJ, Nowick JS, Macrocyclic ?-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide, J Am Chem Soc, 2011, 133 (9), 3144-57.
Zheng Jing, Liu Cong, Sawaya Michael R, Vadla Balraju, Khan Shafiullah, Woods R Jeremy, Eisenberg David, Goux Warren J, Nowick James S, Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide, Journal of the American Chemical Society, 2011, 133 (9), 3144-57.
Colletier Jacques-Philippe, Laganowsky Arthur, Landau Meytal, Zhao Minglei, Soriaga Angela B, Goldschmidt Lukasz, Flot David, Cascio Duilio, Sawaya Michael R, Eisenberg David, Molecular basis for amyloid-beta polymorphism, Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (41), 16938-43.
Eisenberg D., Reflections on the past and future of integrative medicine from a lifelong student of the integration of Chinese and Western medicine, Chin J Integr Med, 2011, 17 (1), 3-5.
Eisenberg D., Reflections on the past and future of integrative medicine from a lifelong student of the integration of Chinese and Western medicine, Chin J Integr Med, 2011, 17 (1), 3-5.
Zhao Minglei, Cascio Duilio, Sawaya Michael R, Eisenberg David, Structures of segments of α-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation, Protein science : a publication of the Protein Society, 2011, 20 (6), 996-1004.
Chim Nicholas, Habel Jeff E, Johnston Jodie M, Krieger Inna, Miallau Linda, Sankaranarayanan Ramasamy, Morse Robert P, Bruning John, Swanson Stephanie, Kim Haelee, Kim Chang-Yub, Li Hongye, Bulloch Esther M, Payne Richard J, Manos-Turvey Alexandra, Hung Li-Wei, Baker Edward N, Lott J Shaun, James Michael N G, Terwilliger Thomas C, Eisenberg David S, Sacchettini James C, Goulding Celia W, The TB Structural Genomics Consortium: a decade of progress, Tuberculosis (Edinburgh, Scotland), 2011, 91 (2), 155-72.
Landau Meytal, Sawaya Michael R, Faull Kym F, Laganowsky Arthur, Jiang Lin, Sievers Stuart A, Liu Jie, Barrio Jorge R, Eisenberg David, Towards a pharmacophore for amyloid, PLoS biology, 2011, 9 (6), e1001080.
Liu Cong, Sawaya Michael R, Eisenberg David, β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages, Nature structural & molecular biology, 2011, 18 (1), 49-55.
Laganowsky Arthur, Benesch Justin L P, Landau Meytal, Ding Linlin, Sawaya Michael R, Cascio Duilio, Huang Qingling, Robinson Carol V, Horwitz Joseph, Eisenberg David, Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function, Protein science : a publication of the Protein Society, 2010, 19 (5), 1031-43.
Apostol MI, Sawaya MR, Cascio D, Eisenberg D, Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease, J Biol Chem. , 2010, 285 (39), 29671-5.
Apostol Marcin I, Sawaya Michael R, Cascio Duilio, Eisenberg David, Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease, The Journal of biological chemistry, 2010, 285 (39), 29671-5.
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.
Ostapchenko Valeriy G, Sawaya Michael R, Makarava Natallia, Savtchenko Regina, Nilsson K Peter R, Eisenberg David, Baskakov Ilia V, Two amyloid States of the prion protein display significantly different folding patterns, Journal of molecular biology, 2010, 400 (4), 908-21.
Khakshoor O, Lin AJ, Korman TP, Sawaya MR, Tsai SC, Eisenberg D, Nowick JS, X-ray crystallographic structure of an artificial beta-sheet dimer, J Am Chem Soc, 2010, 132 (33), 11622-8.
Khakshoor Omid, Lin Aaron J, Korman Tyler P, Sawaya Michael R, Tsai Shiou-Chuan, Eisenberg David, Nowick James S, X-ray crystallographic structure of an artificial beta-sheet dimer, Journal of the American Chemical Society, 2010, 132 (33), 11622-8.
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.
Sawaya Michael R, Wojtowicz Woj M, Andre Ingemar, Qian Bin, Wu Wei, Baker David, Eisenberg David, Zipursky S Lawrence, 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).
Wang Lei, Maji Samir K, Sawaya Michael R, Eisenberg David, Riek Roland, Bacterial inclusion bodies contain amyloid-like structure, PLoS biology, 2008, 6 (8), e195.
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, 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.
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.
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.
Sandra Orchard, Lukasz Salwinski, Samuel Kerrien, Luisa Montecchi-Palazzi, Matthias Oesterheld, Volker Stümpflen, Arnaud Ceol, Andrew Chatr-aryamontri, John Armstrong, Peter Woollard, John J Salama, Susan Moore, Jérôme Wojcik, Gary D Bader, Marc Vidal, Michael E Cusick, Mark Gerstein, Anne-Claude Gavin, Giulio Superti-Furga, Jack Greenblatt, Joel Bader, Peter Uetz, Mike Tyers, Pierre Legrain, Stan Fields, Nicola Mulder, Michael Gilson, Michael Niepmann, Lyle Burgoon, Javier De Las Rivas, Carlos Prieto, Victoria M Perreau, Chris Hogue, Hans-Werner Mewes, Rolf Apweiler, Ioannis Xenarios, David Eisenberg, Gianni Cesareni & Henning Hermjakob, The minimum information required for reporting a molecular interaction experiment (MIMIx), Nature Biotechnology, 2007, 25, 894-8.
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.