Eisenberg, David S.


WebsiteHome URL
Division
Biochemistry
Title
Faculty
Distinguished Professor
P.D. Boyer Chair
Specialties
Biochemistry
Biophysics
Structural and Computational Biology
Bioenergy and the Environment
Proteomics and Bioinformatics
Theory
Member
ACCESS Program: Dept. of Biological Chemistry, California NanoSystems Institute

Contact Information

Email
Office
Boyer Hall 201A
(310) 825-3754
Lab
Boyer Hall 205
(310) 206-3642

Short Biography

David Eisenberg is a 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.

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, and 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.

Research Interest

David Eisenberg and his research group focus on protein interactions. In their experiments they study the structural basis for conversion of normal proteins to the amyloid state and conversion of prions to the infectious state. In bioinformatic work, they derive information on protein interactions from genomic and proteomic data, and design inhibitors of amyloid toxicity.

Amyloid and prion diseases are diseases of protein aggregation in which a normal, functional protein converts to an abnormal, aggregated protein. The systemic amyloid diseases, such as dialysis-related amyloidosis, are apparently caused by the accumulation of fibers until organs fail. The neurodegenerative amyloid diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis (ALS), and the prion conditions, seem to be caused by smaller oligomers, intermediate in size between monomers and fibers. Our goals are to understand the general features of the conversion to the amyloid state, why some of the diseases are transmissible between organisms and others not, what the structures of the toxic units are, and how they exert their toxic actions.

Steric Zipper

In 2005, we determined the atomic-level structure for the spine of an amyloid fiber. This structure shows that the spine consists of two parallel beta sheets, packed across a tight, dry interface that we call a steric zipper. The structure of the spine explains the stability of amyloid, gives hints about the conversion process, and suggests why some proteins form amyloid while others do not. Since 2005, we have determined some 90 amyloid spines from 15 disease-related proteins, using a combination of bioinformatics and structural tools. In 2010, we determined the structure of a small toxic amyloid-related oligomer, consisting of six anti-parallel beta strands forming a cylindrical barrel. This structure may suggest models for the toxic oligomers associated with amyloid diseases.

 

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Honors & Awards

  • 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

Publications

2014

2013

2012

2011

2010

  • Khakshoor O, Lin AJ, Korman TP, Sawaya MR, Tsai SC, Eisenberg D, Nowick JS. (2010). X-ray crystallographic structure of an artificial beta-sheet dimer. J Am Chem Soc.. Aug 2010. 25;132(33): 11622-8 [Abstract]
  • Goldschmidt L, Teng PK, Riek R, Eisenberg D. (2010). Identifying the amylome, proteins capable of forming amyloid-like fibrils.Proc. Natl. Acad. Sci. U.S.A.. Feb 2010. 107(8):3487-92. [Abstract]
  • Laganowsky A, Benesch JL, Landau M, Ding L, Sawaya MR, Cascio D, Huang Q, Robinson CV, Horwitz J, Eisenberg D. (2010). Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function.Protein Sci.. May 2010. 19(5):1031-43. [Abstract]
  • Wang L, Schubert D, Sawaya MR, Eisenberg D, Riek R. (2010). Multidimensional structure-activity relationship of a protein in its aggregated states.Angew. Chem. Int. Ed. Engl.. May 2010. 49(23):3904-8. [Abstract]
  • Khakshoor O, Lin AJ, Korman TP, Sawaya MR, Tsai SC, Eisenberg D, Nowick JS. (2010). X-ray crystallographic structure of an artificial beta-sheet dimer.J. Am. Chem. Soc.. Aug 2010. 132(33):11622-8. [Abstract]
  • Apostol MI, Sawaya MR, Cascio D, Eisenberg D. (2010). 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.. Sep 2010. 285(39):29671-5. [Abstract]
  • Arbing MA, Kaufmann M, Phan T, Chan S, Cascio D, Eisenberg D. (2010). The crystal structure of the Mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer.Protein Sci.. Sep 2010. 19(9):1692-703. [Abstract]
  • Laganowsky A, Eisenberg D. (2010). Non-3D domain swapped crystal structure of truncated zebrafish alphaA crystallin.Protein Sci.. Oct 2010. 19(10):1978-84. [Abstract]

2009

  • Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. (2009). Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.BMC Syst Biol. 2009. 3:115. [Abstract]
  • Miallau L, Faller M, Chiang J, Arbing M, Guo F, Cascio D, Eisenberg D. (2009). Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis.J. Biol. Chem.. Jan 2009. 284(1):276-83. [Abstract]
  • Wiltzius JJ, Sievers SA, Sawaya MR, Eisenberg D. (2009). Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process.Protein Sci.. Jul 2009. 18(7):1521-30. [Abstract]
  • Teng PK, Eisenberg D. (2009). Short protein segments can drive a non-fibrillizing protein into the amyloid state.Protein Eng. Des. Sel.. Aug 2009. 22(8):531-6. [Abstract]
  • Wiltzius JJ, Landau M, Nelson R, Sawaya MR, Apostol MI, Goldschmidt L, Soriaga AB, Cascio D, Rajashankar K, Eisenberg D. (2009). Molecular mechanisms for protein-encoded inheritance.Nat. Struct. Mol. Biol.. Sep 2009. 16(9):973-8. [Abstract]
  • Ivanova MI, Sievers SA, Sawaya MR, Wall JS, Eisenberg D. (2009). Molecular basis for insulin fibril assembly.Proc. Natl. Acad. Sci. U.S.A.. Nov 2009. 106(45):18990-5. [Abstract]
  • Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H. (2009). Recurated protein interaction datasets.Nat. Methods. Dec 2009. 6(12):860-1. [Abstract]

2008

  • Riley R, Pellegrini M, Eisenberg D. (2008). 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):e1000174. [Abstract]
  • Miller CS, Eisenberg D. (2008). Using inferred residue contacts to distinguish between correct and incorrect protein models.Bioinformatics. Jul 2008. 24(14):1575-82. [Abstract]
  • Cruz D, Watson AD, Miller CS, Montoya D, Ochoa MT, Sieling PA, Gutierrez MA, Navab M, Reddy ST, Witztum JL, Fogelman AM, Rea TH, Eisenberg D, Berliner J, Modlin RL. (2008). Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy.J. Clin. Invest.. Aug 2008. 118(8):2917-28. [Abstract]
  • Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R. (2008). Bacterial inclusion bodies contain amyloid-like structure.PLoS Biol.. Aug 2008. 6(8):e195. [Abstract]
  • Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. (2008). A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.Cell. Sep 2008. 134(6):1007-18. [Abstract]
  • Wiltzius JJ, Sievers SA, Sawaya MR, Cascio D, Popov D, Riekel C, Eisenberg D. (2008). Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin).Protein Sci.. Sep 2008. 17(9):1467-74. [Abstract]
  • Guo Z, Eisenberg D. (2008). The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold.Protein Sci.. Sep 2008. 17(9):1617-23. [Abstract]
  • Llewellyn R, Eisenberg DS. (2008). Annotating proteins with generalized functional linkages.Proc. Natl. Acad. Sci. U.S.A.. Nov 2008. 105(46):17700-5. [Abstract]
  • Zhang K, Sawaya MR, Eisenberg DS, Liao JC. (2008). Expanding metabolism for biosynthesis of nonnatural alcohols.Proc. Natl. Acad. Sci. U.S.A.. Dec 2008. 105(52):20653-8. [Abstract]
  • Medrano-Soto A, Pal D, Eisenberg D. (2008). Inferring molecular function: contributions from functional linkages.Trends Genet.. Dec 2008. 24(12):587-90. [Abstract]

2007

  • Strong M, Eisenberg D. (2007). The protein network as a tool for finding novel drug targets.Prog Drug Res. 2007. 64:191, 193-215. [Abstract]
  • Goulding CW, Bowers PM, Segelke B, Lekin T, Kim CY, Terwilliger TC, Eisenberg D. (2007). The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function.J. Mol. Biol.. Jan 2007. 365(2):275-83. [Abstract]
  • Tsemekhman K, Goldschmidt L, Eisenberg D, Baker D. (2007). Cooperative hydrogen bonding in amyloid formation.Protein Sci.. Apr 2007. 16(4):761-4. [Abstract]
  • Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. (2007). Atomic structures of amyloid cross-beta spines reveal varied steric zippers.Nature. May 2007. 447(7143):453-7. [Abstract]
  • Guo Z, Eisenberg D. (2007). The mechanism of the amyloidogenic conversion of T7 endonuclease I.J. Biol. Chem.. May 2007. 282(20):14968-74. [Abstract]
  • Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D. (2007). Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.Protein Sci.. Aug 2007. 16(8):1569-76. [Abstract]
  • Salwinski L, Eisenberg D. (2007). The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.Bioinformatics. Aug 2007. 23(16):2193-5. [Abstract]
  • Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D. (2007). Functional linkages can reveal protein complexes for structure determination.Structure. Sep 2007. 15(9):1079-89. [Abstract]
  • Anderson DH, Kickhoefer VA, Sievers SA, Rome LH, Eisenberg D. (2007). Draft crystal structure of the vault shell at 9-A resolution.PLoS Biol.. Nov 2007. 5(11):e318. [Abstract]
  • Kuriyan J, Eisenberg D. (2007). The origin of protein interactions and allostery in colocalization.Nature. Dec 2007. 450(7172):983-90. [Abstract]

2006

  • Nelson R, Eisenberg D. (2006). Structural models of amyloid-like fibrils.Adv. Protein Chem.. 2006. 73:235-82. [Abstract]
  • Wang S, Eisenberg D. (2006). Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action.Biochemistry. Feb 2006. 45(6):1554-61. [Abstract]
  • Ivanova MI, Thompson MJ, Eisenberg D. (2006). A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments.Proc. Natl. Acad. Sci. U.S.A.. Mar 2006. 103(11):4079-82. [Abstract]
  • Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. (2006). The 3D profile method for identifying fibril-forming segments of proteins.Proc. Natl. Acad. Sci. U.S.A.. Mar 2006. 103(11):4074-8. [Abstract]
  • Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. (2006). Bioinformatic challenges for the next decade(s).Philos. Trans. R. Soc. Lond., B, Biol. Sci.. Mar 2006. 361(1467):525-7. [Abstract]
  • Liu PT, Stenger S, Li H, Wenzel L, Tan BH, Krutzik SR, Ochoa MT, Schauber J, Wu K, Meinken C, Kamen DL, Wagner M, Bals R, Steinmeyer A, Zügel U, Gallo RL, Eisenberg D, Hewison M, Hollis BW, Adams JS, Bloom BR, Modlin RL. (2006). Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response.Science. Mar 2006. 311(5768):1770-3. [Abstract]
  • Nelson R, Eisenberg D. (2006). Recent atomic models of amyloid fibril structure.Curr. Opin. Struct. Biol.. Apr 2006. 16(2):260-5. [Abstract]
  • Guo Z, Eisenberg D. (2006). Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I.Proc. Natl. Acad. Sci. U.S.A.. May 2006. 103(21):8042-7. [Abstract]
  • Bennett MJ, Sawaya MR, Eisenberg D. (2006). Deposition diseases and 3D domain swapping.Structure. May 2006. 14(5):811-24. [Abstract]
  • Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D. (2006). Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.Proc. Natl. Acad. Sci. U.S.A.. May 2006. 103(21):8060-5. [Abstract]
  • Eisenberg D, Nelson R, Sawaya MR, Balbirnie M, Sambashivan S, Ivanova MI, Madsen AØ, Riekel C. (2006). The structural biology of protein aggregation diseases: Fundamental questions and some answers.Acc. Chem. Res.. Sep 2006. 39(9):568-75. [Abstract]

2005

  • Riley R, Lee C, Sabatti C, Eisenberg D. (2005). Inferring protein domain interactions from databases of interacting proteins.Genome Biol.. 2005. 6(10):R89. [Abstract]
  • Pal D, Eisenberg D. (2005). Inference of protein function from protein structure.Structure. Jan 2005. 13(1):121-30. [Abstract]
  • Li H, Pellegrini M, Eisenberg D. (2005). Detection of parallel functional modules by comparative analysis of genome sequences.Nat. Biotechnol.. Feb 2005. 23(2):253-60. [Abstract]
  • Müller P, Sawaya MR, Pashkov I, Chan S, Nguyen C, Wu Y, Perry LJ, Eisenberg D. (2005). The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.Acta Crystallogr. D Biol. Crystallogr.. Mar 2005. 61(Pt 3):309-15. [Abstract]
  • Li H, Sawaya MR, Tabita FR, Eisenberg D. (2005). Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum.Structure. May 2005. 13(5):779-89. [Abstract]
  • Goulding CW, Apostol MI, Sawaya MR, Phillips M, Parseghian A, Eisenberg D. (2005). Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme.J. Mol. Biol.. May 2005. 349(1):61-72. [Abstract]
  • Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. (2005). Structure of the cross-beta spine of amyloid-like fibrils.Nature. Jun 2005. 435(7043):773-8. [Abstract]
  • Sambashivan S, Liu Y, Sawaya MR, Gingery M, Eisenberg D. (2005). Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure.Nature. Sep 2005. 437(7056):266-9. [Abstract]
  • Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D. (2005). Utilizing logical relationships in genomic data to decipher cellular processes.FEBS J.. Oct 2005. 272(20):5110-8. [Abstract]

2004

  • Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. (2004). Prolinks: a database of protein functional linkages derived from coevolution.Genome Biol.. 2004. 5(5):R35. [Abstract]
  • Kleiger G, Panina EM, Mallick P, Eisenberg D. (2004). PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence.Protein Sci.. Jan 2004. 13(1):221-9. [Abstract]
  • Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. (2004). The Database of Interacting Proteins: 2004 update.Nucleic Acids Res.. Jan 2004. 32(Database issue):D449-51. [Abstract]
  • Goulding CW, Apostol MI, Gleiter S, Parseghian A, Bardwell J, Gennaro M, Eisenberg D. (2004). Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis.J. Biol. Chem.. Jan 2004. 279(5):3516-24. [Abstract]
  • Ivanova MI, Sawaya MR, Gingery M, Attinger A, Eisenberg D. (2004). An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril.Proc. Natl. Acad. Sci. U.S.A.. Jul 2004. 101(29):10584-9. [Abstract]
  • Salwinski L, Eisenberg D. (2004). In silico simulation of biological network dynamics.Nat. Biotechnol.. Aug 2004. 22(8):1017-9. [Abstract]
  • Reinhardt A, Eisenberg D. (2004). DPANN: improved sequence to structure alignments following fold recognition.Proteins. Aug 2004. 56(3):528-38. [Abstract]
  • Bowers PM, Cokus SJ, Eisenberg D, Yeates TO. (2004). Use of logic relationships to decipher protein network organization.Science. Dec 2004. 306(5705):2246-9. [Abstract]

2003

  • Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. (2003). 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. [Abstract]
  • Eisenberg D. (2003). John T. Edsall as tutor and teacher.Biophys. Chem.. 2003. 100(1-3):91-3. [Abstract]
  • Anderson DH, Sawaya MR, Cascio D, Ernst W, Modlin R, Krensky A, Eisenberg D. (2003). Granulysin crystal structure and a structure-derived lytic mechanism.J. Mol. Biol.. Jan 2003. 325(2):355-65. [Abstract]
  • McCarty AS, Kleiger G, Eisenberg D, Smale ST. (2003). Selective dimerization of a C2H2 zinc finger subfamily.Mol. Cell. Feb 2003. 11(2):459-70. [Abstract]
  • Mura C, Katz JE, Clarke SG, Eisenberg D. (2003). Structure and function of an archaeal homolog of survival protein E (SurEalpha): an acid phosphatase with purine nucleotide specificity.J. Mol. Biol.. Mar 2003. 326(5):1559-75. [Abstract]
  • Mura C, Phillips M, Kozhukhovsky A, Eisenberg D. (2003). Structure and assembly of an augmented Sm-like archaeal protein 14-mer.Proc. Natl. Acad. Sci. U.S.A.. Apr 2003. 100(8):4539-44. [Abstract]
  • Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D. (2003). The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs).Protein Sci.. Apr 2003. 12(4):832-47. [Abstract]
  • Wang S, Eisenberg D. (2003). Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate.Protein Sci.. May 2003. 12(5):1097-108. [Abstract]
  • Salwinski L, Eisenberg D. (2003). Computational methods of analysis of protein-protein interactions.Curr. Opin. Struct. Biol.. Jun 2003. 13(3):377-82. [Abstract]
  • Freedland SJ, Pantuck AJ, Paik SH, Zisman A, Graeber TG, Eisenberg D, McBride WH, Nguyen D, Tso CL, Belldegrun AS. (2003). Heterogeneity of molecular targets on clonal cancer lines derived from a novel hormone-refractory prostate cancer tumor system.Prostate. Jun 2003. 55(4):299-307. [Abstract]
  • Goulding CW, Perry LJ, Anderson D, Sawaya MR, Cascio D, Apostol MI, Chan S, Parseghian A, Wang SS, Wu Y, Cassano V, Gill HS, Eisenberg D. (2003). Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA.Biophys. Chem.. Sep 2003. 105(2-3):361-70. [Abstract]
  • Bleharski JR, Li H, Meinken C, Graeber TG, Ochoa MT, Yamamura M, Burdick A, Sarno EN, Wagner M, Röllinghoff M, Rea TH, Colonna M, Stenger S, Bloom BR, Eisenberg D, Modlin RL. (2003). Use of genetic profiling in leprosy to discriminate clinical forms of the disease.Science. Sep 2003. 301(5639):1527-30. [Abstract]
  • Eisenberg D. (2003). The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.Proc. Natl. Acad. Sci. U.S.A.. Sep 2003. 100(20):11207-10. [Abstract]
  • Lee S, Eisenberg D. (2003). Seeded conversion of recombinant prion protein to a disulfide-bonded oligomer by a reduction-oxidation process.Nat. Struct. Biol.. Sep 2003. 10(9):725-30. [Abstract]
  • Ivanova MI, Gingery M, Whitson LJ, Eisenberg D. (2003). Role of the C-terminal 28 residues of beta2-microglobulin in amyloid fibril formation.Biochemistry. Nov 2003. 42(46):13536-40. [Abstract]
  • Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. (2003). Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps.Nucleic Acids Res.. Dec 2003. 31(24):7099-109. [Abstract]
  • Lee S, Sawaya MR, Eisenberg D. (2003). Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning.Acta Crystallogr. D Biol. Crystallogr.. Dec 2003. 59(Pt 12):2191-9. [Abstract]

2002

  • Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D. (2002). DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.Nucleic Acids Res.. Jan 2002. 30(1):303-5. [Abstract]
  • Duan XJ, Xenarios I, Eisenberg D. (2002). Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database.Mol. Cell Proteomics. Feb 2002. 1(2):104-16. [Abstract]
  • Liu Y, Gotte G, Libonati M, Eisenberg D. (2002). Structures of the two 3D domain-swapped RNase A trimers.Protein Sci.. Feb 2002. 11(2):371-80. [Abstract]
  • Wang S, Mura C, Sawaya MR, Cascio D, Eisenberg D. (2002). Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.Acta Crystallogr. D Biol. Crystallogr.. Apr 2002. 58(Pt 4):571-8. [Abstract]
  • Deane CM, Salwiński Ł, Xenarios I, Eisenberg D. (2002). Protein interactions: two methods for assessment of the reliability of high throughput observations.Mol. Cell Proteomics. May 2002. 1(5):349-56. [Abstract]
  • Kleiger G, Grothe R, Mallick P, Eisenberg D. (2002). GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles.Biochemistry. May 2002. 41(19):5990-7. [Abstract]
  • Goulding CW, Sawaya MR, Parseghian A, Lim V, Eisenberg D, Missiakas D. (2002). Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD.Biochemistry. Jun 2002. 41(22):6920-7. [Abstract]
  • Liu Y, Eisenberg D. (2002). 3D domain swapping: as domains continue to swap.Protein Sci.. Jun 2002. 11(6):1285-99. [Abstract]
  • Mallick P, Boutz DR, Eisenberg D, Yeates TO. (2002). Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.Proc. Natl. Acad. Sci. U.S.A.. Jul 2002. 99(15):9679-84. [Abstract]
  • Gill HS, Pfluegl GM, Eisenberg D. (2002). Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation.Biochemistry. Aug 2002. 41(31):9863-72. [Abstract]
  • Kleiger G, Eisenberg D. (2002). 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.. Oct 2002. 323(1):69-76. [Abstract]
  • Mallick P, Weiss R, Eisenberg D. (2002). 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.. Dec 2002. 99(25):16041-6. [Abstract]
  • Goulding CW, Parseghian A, Sawaya MR, Cascio D, Apostol MI, Gennaro ML, Eisenberg D. (2002). Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution.Protein Sci.. Dec 2002. 11(12):2887-93. [Abstract]

2001

  • Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, Marcotte EM, Eisenberg D. (2001). DIP: The Database of Interacting Proteins: 2001 update.Nucleic Acids Res.. Jan 2001. 29(1):239-41. [Abstract]
  • Gill HS, Eisenberg D. (2001). The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition.Biochemistry. Feb 2001. 40(7):1903-12. [Abstract]
  • Balbirnie M, Grothe R, Eisenberg DS. (2001). An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid.Proc. Natl. Acad. Sci. U.S.A.. Feb 2001. 98(5):2375-80. [Abstract]
  • Ogihara NL, Ghirlanda G, Bryson JW, Gingery M, DeGrado WF, Eisenberg D. (2001). Design of three-dimensional domain-swapped dimers and fibrous oligomers.Proc. Natl. Acad. Sci. U.S.A.. Feb 2001. 98(4):1404-9. [Abstract]
  • Anderson DH, Harth G, Horwitz MA, Eisenberg D. (2001). An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B), a mycolyl transferase.J. Mol. Biol.. Mar 2001. 307(2):671-81. [Abstract]
  • Liu Y, Gotte G, Libonati M, Eisenberg D. (2001). A domain-swapped RNase A dimer with implications for amyloid formation.Nat. Struct. Biol.. Mar 2001. 8(3):211-4. [Abstract]
  • Marcotte EM, Xenarios I, Eisenberg D. (2001). Mining literature for protein-protein interactions.Bioinformatics. Apr 2001. 17(4):359-63. [Abstract]
  • Landgraf R, Xenarios I, Eisenberg D. (2001). Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.J. Mol. Biol.. Apr 2001. 307(5):1487-502. [Abstract]
  • Mura C, Cascio D, Sawaya MR, Eisenberg DS. (2001). The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core.Proc. Natl. Acad. Sci. U.S.A.. May 2001. 98(10):5532-7. [Abstract]
  • Xenarios I, Eisenberg D. (2001). Protein interaction databases.Curr. Opin. Biotechnol.. Aug 2001. 12(4):334-9. [Abstract]
  • Dym O, Eisenberg D. (2001). Sequence-structure analysis of FAD-containing proteins.Protein Sci.. Sep 2001. 10(9):1712-28. [Abstract]
  • Graeber TG, Eisenberg D. (2001). Bioinformatic identification of potential autocrine signaling loops in cancers from gene expression profiles.Nat. Genet.. Nov 2001. 29(3):295-300. [Abstract]
  • Singer E, Landgraf R, Horan T, Slamon D, Eisenberg D. (2001). Identification of a heregulin binding site in HER3 extracellular domain.J. Biol. Chem.. Nov 2001. 276(47):44266-74. [Abstract]
  • Kleiger G, Perry J, Eisenberg D. (2001). 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. Dec 2001. 40(48):14484-92. [Abstract]
  • Salwinski L, Eisenberg D. (2001). Motif-based fold assignment.Protein Sci.. Dec 2001. 10(12):2460-9. [Abstract]

2000

  • Diehl DL, Eisenberg D. (2000). Complementary and alternative medicine (CAM): epidemiology and implications for research.Prog. Brain Res.. 2000. 122:445-55. [Abstract]
  • Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. (2000). DIP: the database of interacting proteins.Nucleic Acids Res.. Jan 2000. 28(1):289-91. [Abstract]
  • Eisenberg D, Gill HS, Pfluegl GM, Rotstein SH. (2000). Structure-function relationships of glutamine synthetases.Biochim. Biophys. Acta. Mar 2000. 1477(1-2):122-45. [Abstract]
  • Mallick P, Goodwill KE, Fitz-Gibbon S, Miller JH, Eisenberg D. (2000). Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing.Proc. Natl. Acad. Sci. U.S.A.. Mar 2000. 97(6):2450-5. [Abstract]
  • Ruth L, Eisenberg D, Neufeld EF. (2000). alpha-L-iduronidase forms semi-crystalline spherulites with amyloid-like properties.Acta Crystallogr. D Biol. Crystallogr.. Apr 2000. 56(Pt 4):524-8. [Abstract]
  • Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. (2000). Protein function in the post-genomic era.Nature. Jun 2000. 405(6788):823-6. [Abstract]
  • Kleiger G, Beamer LJ, Grothe R, Mallick P, Eisenberg D. (2000). The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold.J. Mol. Biol.. Jun 2000. 299(4):1019-34. [Abstract]
  • Landgraf R, Eisenberg D. (2000). Heregulin reverses the oligomerization of HER3.Biochemistry. Jul 2000. 39(29):8503-11. [Abstract]
  • Dym O, Pratt EA, Ho C, Eisenberg D. (2000). The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme.Proc. Natl. Acad. Sci. U.S.A.. Aug 2000. 97(17):9413-8. [Abstract]
  • Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. (2000). Localizing proteins in the cell from their phylogenetic profiles.Proc. Natl. Acad. Sci. U.S.A.. Oct 2000. 97(22):12115-20. [Abstract]
  • Steere B, Eisenberg D. (2000). Characterization of high-order diphtheria toxin oligomers.Biochemistry. Dec 2000. 39(51):15901-9. [Abstract]

1999

  • Marcotte EM, Eisenberg D. (1999). Chicken prion tandem repeats form a stable, protease-resistant domain.Biochemistry. Jan 1999. 38(2):667-76. [Abstract]
  • Hart PJ, Balbirnie MM, Ogihara NL, Nersissian AM, Weiss MS, Valentine JS, Eisenberg D. (1999). A structure-based mechanism for copper-zinc superoxide dismutase.Biochemistry. Feb 1999. 38(7):2167-78. [Abstract]
  • Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. (1999). Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.Proc. Natl. Acad. Sci. U.S.A.. Apr 1999. 96(8):4285-8. [Abstract]
  • Gill HS, Pfluegl GM, Eisenberg D. (1999). Preliminary crystallographic studies on glutamine synthetase from Mycobacterium tuberculosis.Acta Crystallogr. D Biol. Crystallogr.. Apr 1999. 55(Pt 4):865-8. [Abstract]
  • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. (1999). Detecting protein function and protein-protein interactions from genome sequences.Science. Jul 1999. 285(5428):751-3. [Abstract]
  • Patterson WR, Anderson DH, DeGrado WF, Cascio D, Eisenberg D. (1999). Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.Protein Sci.. Jul 1999. 8(7):1410-22. [Abstract]
  • Thompson MJ, Eisenberg D. (1999). Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability.J. Mol. Biol.. Jul 1999. 290(2):595-604. [Abstract]
  • Eisenberg D. (1999). How chaperones protect virgin proteins.Science. Aug 1999. 285(5430):1021-2. [Abstract]
  • Eisenberg D. (1999). Glories of protein structureStructure. Oct 1999. 7(10):R241-2. [Abstract]
  • Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D. (1999). A census of protein repeats.J. Mol. Biol.. Oct 1999. 293(1):151-60. [Abstract]
  • Landgraf R, Fischer D, Eisenberg D. (1999). Analysis of heregulin symmetry by weighted evolutionary tracing.Protein Eng.. Nov 1999. 12(11):943-51. [Abstract]
  • Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. (1999). A combined algorithm for genome-wide prediction of protein function.Nature. Nov 1999. 402(6757):83-6. [Abstract]

1998

  • Liu Y, Hart PJ, Schlunegger MP, Eisenberg D. (1998). The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution.Proc. Natl. Acad. Sci. U.S.A.. Mar 1998. 95(7):3437-42. [Abstract]
  • Hart PJ, Liu H, Pellegrini M, Nersissian AM, Gralla EB, Valentine JS, Eisenberg D. (1998). Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis.Protein Sci.. Mar 1998. 7(3):545-55. [Abstract]
  • Landgraf R, Pegram M, Slamon DJ, Eisenberg D. (1998). Cytotoxicity and specificity of directed toxins composed of diphtheria toxin and the EGF-like domain of heregulin beta1.Biochemistry. Mar 1998. 37(9):3220-8. [Abstract]
  • Beamer LJ, Carroll SF, Eisenberg D. (1998). The BPI/LBP family of proteins: a structural analysis of conserved regions.Protein Sci.. Apr 1998. 7(4):906-14. [Abstract]
  • Peer Bork, David Eisenberg. (1998). Sequences and topology Deriving biological knowledge from genomic sequences Curr. Opin. Struct. Biol.. June 1998. 8(3): 331-332 [Abstract]
  • Beamer LJ, Fischer D, Eisenberg D. (1998). Detecting distant relatives of mammalian LPS-binding and lipid transport proteins.Protein Sci.. Jul 1998. 7(7):1643-6. [Abstract]

1997

  • Rice DW, Fischer D, Weiss R, Eisenberg D. (1997). Fold assignments for amino acid sequences of the CASP2 experiment.Proteins. 1997. Suppl 1:113-22. [Abstract]
  • Eisenberg D, Lüthy R, Bowie JU. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles.Meth. Enzymol.. 1997. 277:396-404. [Abstract]
  • Schlunegger MP, Bennett MJ, Eisenberg D. (1997). Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly.Adv. Protein Chem.. 1997. 50:61-122. [Abstract]
  • Bell CE, Eisenberg D. (1997). Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.Adv. Exp. Med. Biol.. 1997. 419:35-43. [Abstract]
  • Bell CE, Eisenberg D. (1997). Crystal structure of nucleotide-free diphtheria toxin.Biochemistry. Jan 1997. 36(3):481-8. [Abstract]
  • Ogihara NL, Weiss MS, Degrado WF, Eisenberg D. (1997). The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies.Protein Sci.. Jan 1997. 6(1):80-8. [Abstract]
  • Eisenberg D. (1997). Into the black of night.Nat. Struct. Biol.. Feb 1997. 4(2):95-7. [Abstract]
  • Rice DW, Eisenberg D. (1997). A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.J. Mol. Biol.. Apr 1997. 267(4):1026-38. [Abstract]
  • Beamer LJ, Carroll SF, Eisenberg D. (1997). Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution.Science. Jun 1997. 276(5320):1861-4. [Abstract]
  • Anderson DH, Weiss MS, Eisenberg D. (1997). Charges, hydrogen bonds, and correlated motions in the 1 A resolution refined structure of the mating pheromone Er-1 from Euplotes raikovi.J. Mol. Biol.. Oct 1997. 273(2):479-500. [Abstract]
  • Fischer D, Eisenberg D. (1997). Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium.Proc. Natl. Acad. Sci. U.S.A.. Oct 1997. 94(22):11929-34. [Abstract]
  • Bell CE, Yeates TO, Eisenberg D. (1997). Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes.Protein Sci.. Oct 1997. 6(10):2084-96. [Abstract]
  • Bell CE, Poon PH, Schumaker VN, Eisenberg D. (1997). Oligomerization of a 45 kilodalton fragment of diphtheria toxin at pH 5.0 to a molecule of 20-24 subunits.Biochemistry. Dec 1997. 36(49):15201-7. [Abstract]

1996

  • Fischer D, Elofsson A, Rice D, Eisenberg D. (1996). Assessing the performance of fold recognition methods by means of a comprehensive benchmark.Pac Symp Biocomput. 1996. :300-18. [Abstract]
  • Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D. (1996). A study of combined structure/sequence profiles.Fold Des. 1996. 1(6):451-61. [Abstract]
  • Bowie JU, Zhang K, Wilmanns M, Eisenberg D. (1996). Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure.Meth. Enzymol.. 1996. 266:598-616. [Abstract]
  • Bell CE, Eisenberg D. (1996). Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.Biochemistry. Jan 1996. 35(4):1137-49. [Abstract]
  • Fischer D, Rice D, Bowie JU, Eisenberg D. (1996). Assigning amino acid sequences to 3-dimensional protein folds.FASEB J.. Jan 1996. 10(1):126-36. [Abstract]
  • Ogihara NL, Parge HE, Hart PJ, Weiss MS, Goto JJ, Crane BR, Tsang J, Slater K, Roe JA, Valentine JS, Eisenberg D, Tainer JA. (1996). Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase.Biochemistry. Feb 1996. 35(7):2316-21. [Abstract]
  • Anderson DH, Weiss MS, Eisenberg D. (1996). A challenging case for protein crystal structure determination: the mating pheromone Er-1 from Euplotes raikovi.Acta Crystallogr. D Biol. Crystallogr.. May 1996. 52(Pt 3):469-80. [Abstract]
  • Fischer D, Eisenberg D. (1996). Protein fold recognition using sequence-derived predictions.Protein Sci.. May 1996. 5(5):947-55. [Abstract]
  • Fahrner RL, Dieckmann T, Harwig SS, Lehrer RI, Eisenberg D, Feigon J. (1996). Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes.Chem. Biol.. Jul 1996. 3(7):543-50. [Abstract]
  • Hart PJ, Nersissian AM, Herrmann RG, Nalbandyan RM, Valentine JS, Eisenberg D. (1996). A missing link in cupredoxins: crystal structure of cucumber stellacyanin at 1.6 A resolution.Protein Sci.. Nov 1996. 5(11):2175-83. [Abstract]

1995

  • Weiss MS, Blanke SR, Collier RJ, Eisenberg D. (1995). Structure of the isolated catalytic domain of diphtheria toxin.Biochemistry. Jan 1995. 34(3):773-81. [Abstract]
  • Wilmanns M, Eisenberg D. (1995). Inverse protein folding by the residue pair preference profile method: estimating the correctness of alignments of structurally compatible sequences.Protein Eng.. Jul 1995. 8(7):627-39. [Abstract]
  • Vrielink A, Beamer L, Le T, Eisenberg D. (1995). Crystallization of the chaperone protein SecB.Protein Sci.. Aug 1995. 4(8):1651-3. [Abstract]
  • Elofsson A, Le Grand SM, Eisenberg D. (1995). Local moves: an efficient algorithm for simulation of protein folding.Proteins. Sep 1995. 23(1):73-82. [Abstract]
  • Weiss MS, Anderson DH, Raffioni S, Bradshaw RA, Ortenzi C, Luporini P, Eisenberg D. (1995). A cooperative model for receptor recognition and cell adhesion: evidence from the molecular packing in the 1.6-A crystal structure of the pheromone Er-1 from the ciliated protozoan Euplotes raikovi.Proc. Natl. Acad. Sci. U.S.A.. Oct 1995. 92(22):10172-6. [Abstract]
  • Bennett MJ, Schlunegger MP, Eisenberg D. (1995). 3D domain swapping: a mechanism for oligomer assembly.Protein Sci.. Dec 1995. 4(12):2455-68. [Abstract]

1994

  • Liaw SH, Eisenberg D. (1994). Structural model for the reaction mechanism of glutamine synthetase, based on five crystal structures of enzyme-substrate complexes.Biochemistry. Jan 1994. 33(3):675-81. [Abstract]
  • Zhang KY, Cascio D, Eisenberg D. (1994). Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.Protein Sci.. Jan 1994. 3(1):64-9. [Abstract]
  • Bennett MJ, Choe S, Eisenberg D. (1994). Domain swapping: entangling alliances between proteins.Proc. Natl. Acad. Sci. U.S.A.. Apr 1994. 91(8):3127-31. [Abstract]
  • McKenna MC, Muchardt C, Gaynor R, Eisenberg D. (1994). Preparative scale culture of Escherichia coli cells expressing the human immunodeficiency virus type 1 Tat protein.Protein Expr. Purif.. Apr 1994. 5(2):105-11. [Abstract]
  • Zhang KY, Eisenberg D. (1994). The three-dimensional profile method using residue preference as a continuous function of residue environment.Protein Sci.. Apr 1994. 3(4):687-95. [Abstract]
  • Bowie JU, Eisenberg D. (1994). An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.Proc. Natl. Acad. Sci. U.S.A.. May 1994. 91(10):4436-40. [Abstract]
  • Zhang KY, Eisenberg D. (1994). Solid-state phase transition in the crystal structure of ribulose 1,5-bisphosphate carboxylase/oxygenase.Acta Crystallogr. D Biol. Crystallogr.. May 1994. 50(Pt 3):258-62. [Abstract]
  • McKenna MC, Anderson D, Cascio D, Eisenberg D. (1994). Crystallization studies of the human immunodeficiency virus (HIV-1) Tat protein and its trans-activation response element (TAR) RNA.Acta Crystallogr. D Biol. Crystallogr.. Jul 1994. 50(Pt 4):527-34. [Abstract]
  • Privé GG, Verner GE, Weitzman C, Zen KH, Eisenberg D, Kaback HR. (1994). Fusion proteins as tools for crystallization: the lactose permease from Escherichia coli.Acta Crystallogr. D Biol. Crystallogr.. Jul 1994. 50(Pt 4):375-9. [Abstract]
  • Bennett MJ, Eisenberg D. (1994). Refined structure of monomeric diphtheria toxin at 2.3 A resolution.Protein Sci.. Sep 1994. 3(9):1464-75. [Abstract]
  • Bennett MJ, Choe S, Eisenberg D. (1994). Refined structure of dimeric diphtheria toxin at 2.0 A resolution.Protein Sci.. Sep 1994. 3(9):1444-63. [Abstract]
  • Eisenberg D. (1994). Max Perutz's achievements: how did he do it?Protein Sci.. Oct 1994. 3(10):1625-8. [Abstract]

1993

  • Lovejoy B, Choe S, Cascio D, McRorie DK, DeGrado WF, Eisenberg D. (1993). Crystal structure of a synthetic triple-stranded alpha-helical bundle.Science. Feb 1993. 259(5099):1288-93. [Abstract]
  • Wilmanns M, Eisenberg D. (1993). Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.Proc. Natl. Acad. Sci. U.S.A.. Feb 1993. 90(4):1379-83. [Abstract]
  • Liaw SH, Jun G, Eisenberg D. (1993). Extending the diffraction limit of protein crystals: the example of glutamine synthetase from Salmonella typhimurium in the presence of its cofactor ATP.Protein Sci.. Mar 1993. 2(3):470-1. [Abstract]
  • Liaw SH, Pan C, Eisenberg D. (1993). Feedback inhibition of fully unadenylylated glutamine synthetase from Salmonella typhimurium by glycine, alanine, and serine.Proc. Natl. Acad. Sci. U.S.A.. Jun 1993. 90(11):4996-5000. [Abstract]
  • Hill CP, Osslund TD, Eisenberg D. (1993). The structure of granulocyte-colony-stimulating factor and its relationship to other growth factors.Proc. Natl. Acad. Sci. U.S.A.. Jun 1993. 90(11):5167-71. [Abstract]
  • Schreuder HA, Knight S, Curmi PM, Andersson I, Cascio D, Sweet RM, Brändén CI, Eisenberg D. (1993). Crystal structure of activated tobacco rubisco complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate.Protein Sci.. Jul 1993. 2(7):1136-46. [Abstract]
  • Liaw SH, Villafranca JJ, Eisenberg D. (1993). A model for oxidative modification of glutamine synthetase, based on crystal structures of mutant H269N and the oxidized enzyme.Biochemistry. Aug 1993. 32(31):7999-8003. [Abstract]
  • Fujii G, Selsted ME, Eisenberg D. (1993). Defensins promote fusion and lysis of negatively charged membranes.Protein Sci.. Aug 1993. 2(8):1301-12. [Abstract]
  • Schreuder HA, Knight S, Curmi PM, Andersson I, Cascio D, Brändén CI, Eisenberg D. (1993). Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form.Proc. Natl. Acad. Sci. U.S.A.. Nov 1993. 90(21):9968-72. [Abstract]
  • Lovejoy B, Cascio D, Eisenberg D. (1993). Crystal structure of canine and bovine granulocyte-colony stimulating factor (G-CSF).J. Mol. Biol.. Dec 1993. 234(3):640-53. [Abstract]

1992

  • Eisenberg D, Bowie JU, Lüthy R, Choe S. (1992). Three-dimensional profiles for analysing protein sequence-structure relationships.Faraday Discuss.. 1992. (93):25-34. [Abstract]
  • Wesson L, Eisenberg D. (1992). Atomic solvation parameters applied to molecular dynamics of proteins in solution.Protein Sci.. Feb 1992. 1(2):227-35. [Abstract]
  • Lüthy R, Bowie JU, Eisenberg D. (1992). Assessment of protein models with three-dimensional profiles.Nature. Mar 1992. 356(6364):83-5. [Abstract]
  • Choe S, Bennett MJ, Fujii G, Curmi PM, Kantardjieff KA, Collier RJ, Eisenberg D. (1992). The crystal structure of diphtheria toxin.Nature. May 1992. 357(6375):216-22. [Abstract]
  • Wilcox W, Eisenberg D. (1992). Thermodynamics of melittin tetramerization determined by circular dichroism and implications for protein folding.Protein Sci.. May 1992. 1(5):641-53. [Abstract]
  • Lovejoy B, Le TC, Lüthy R, Cascio D, O'Neil KT, DeGrado WF, Eisenberg D. (1992). X-ray grade crystals of a designed alpha-helical coiled coil.Protein Sci.. Jul 1992. 1(7):956-7. [Abstract]
  • Curmi PM, Cascio D, Sweet RM, Eisenberg D, Schreuder H. (1992). Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution.J. Biol. Chem.. Aug 1992. 267(24):16980-9. [Abstract]
  • Liu Y, Peter D, Roghani A, Schuldiner S, Privé GG, Eisenberg D, Brecha N, Edwards RH. (1992). A cDNA that suppresses MPP+ toxicity encodes a vesicular amine transporter.Cell. Aug 1992. 70(4):539-51. [Abstract]
  • Lovejoy B, Akerfeldt KS, DeGrado WF, Eisenberg D. (1992). Crystallization of proton channel peptides.Protein Sci.. Aug 1992. 1(8):1073-7. [Abstract]
  • Fujii G, Horvath S, Woodward S, Eiserling F, Eisenberg D. (1992). A molecular model for membrane fusion based on solution studies of an amphiphilic peptide from HIV gp41.Protein Sci.. Nov 1992. 1(11):1454-64. [Abstract]

1991

  • Lüthy R, McLachlan AD, Eisenberg D. (1991). Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities.Proteins. 1991. 10(3):229-39. [Abstract]
  • Hill CP, Yee J, Selsted ME, Eisenberg D. (1991). Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization.Science. Mar 1991. 251(5000):1481-5. [Abstract]
  • Bowie JU, Lüthy R, Eisenberg D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure.Science. Jul 1991. 253(5016):164-70. [Abstract]
  • Fujii G, Choe SH, Bennett MJ, Eisenberg D. (1991). Crystallization of diphtheria toxin.J. Mol. Biol.. Dec 1991. 222(4):861-4. [Abstract]

1990

  • Eisenberg D, Wesson M. (1990). The most highly amphiphilic alpha-helices include two amino acid segments in human immunodeficiency virus glycoprotein 41.Biopolymers. Jan 1990. 29(1):171-7. [Abstract]
  • Hill CP, Anderson DH, Wesson L, DeGrado WF, Eisenberg D. (1990). Crystal structure of alpha 1: implications for protein design.Science. Aug 1990. 249(4968):543-6. [Abstract]
  • Yamashita MM, Wesson L, Eisenman G, Eisenberg D. (1990). Where metal ions bind in proteins.Proc. Natl. Acad. Sci. U.S.A.. Aug 1990. 87(15):5648-52. [Abstract]
  • Anderson D, Raffioni S, Luporini P, Bradshaw RA, Eisenberg D. (1990). Crystallization of the Euplotes raikovi mating pheromone Er-1.J. Mol. Biol.. Nov 1990. 216(1):1-2. [Abstract]

1989

  • Kantardjieff K, Collier RJ, Eisenberg D. (1989). X-ray grade crystals of the enzymatic fragment of diphtheria toxin.J. Biol. Chem.. Jun 1989. 264(18):10402-4. [Abstract]
  • Rees DC, DeAntonio L, Eisenberg D. (1989). Hydrophobic organization of membrane proteins.Science. Aug 1989. 245(4917):510-3. [Abstract]
  • Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg D. (1989). Refined atomic model of glutamine synthetase at 3.5 A resolution.J. Biol. Chem.. Oct 1989. 264(30):17681-90. [Abstract]

1988

  • Gribskov M, Homyak M, Edenfield J, Eisenberg D. (1988). Profile scanning for three-dimensional structural patterns in protein sequences.Comput. Appl. Biosci.. Mar 1988. 4(1):61-6. [Abstract]
  • Silberman H, Eisenberg D, Ryan J, Shofler R, Niland J, Kaptein E, Nicoloff J, Spencer C. (1988). The relation of thyroid indices in the critically ill patient to prognosis and nutritional factors.Surg Gynecol Obstet. Mar 1988. 166(3):223-8. [Abstract]
  • Chapman MS, Suh SW, Curmi PM, Cascio D, Smith WW, Eisenberg DS. (1988). Tertiary structure of plant RuBisCO: domains and their contacts.Science. Jul 1988. 241(4861):71-4. [Abstract]
  • Hermanson GG, Eisenberg D, Kincade PW, Wall R. (1988). B29: a member of the immunoglobulin gene superfamily exclusively expressed on beta-lineage cells.Proc. Natl. Acad. Sci. U.S.A.. Sep 1988. 85(18):6890-4. [Abstract]

1987

  • Eisenberg D, Almassy RJ, Janson CA, Chapman MS, Suh SW, Cascio D, Smith WW. (1987). Some evolutionary relationships of the primary biological catalysts glutamine synthetase and RuBisCO.Cold Spring Harb. Symp. Quant. Biol.. 1987. 52:483-90. [Abstract]
  • Suh SW, Cascio D, Chapman MS, Eisenberg D. (1987). A crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum in the activated state.J. Mol. Biol.. Sep 1987. 197(2):363-5. [Abstract]

1986

  • Eisenberg D, Wilcox W, Eshita SM, Pryciak PM, Ho SP, DeGrado WF. (1986). The design, synthesis, and crystallization of an alpha-helical peptide.Proteins. Sep 1986. 1(1):16-22. [Abstract]

1977

  • Baker TS, Suh SW, Eisenberg D. (1977). Structure of ribulose-1,5-bisphosphate carboxylase-oxygenase: Form III crystals.Proc. Natl. Acad. Sci. U.S.A.. Mar 1977. 74(3):1037-41. [Abstract]
  • Baker TS, Suh SW, Eisenberg D. (1977). Structure of ribulose-1,5-bisphosphate carboxylase-oxygenase: Form III crystals.Proc. Natl. Acad. Sci. U.S.A.. Mar 1977. 74(3):1037-41. [Abstract]
  • Baker TS, Eisenberg D, Eiserling F. (1977). Ribulose bisphosphate carboxylase: a two-layered, square-shaped molecule of symmetry 422.Science. Apr 1977. 196(4287):293-5. [Abstract]

1976

1975

  • Baker TS, Eisenberg D, Eiserling FA, Weissman L. (1975). The structure of form I crystals of D-ribulose-1,5-diphosphate carboxylase.J. Mol. Biol.. Feb 1975. 91(4):391-9. [Abstract]
  • Frey TG, Eisenberg D, Eiserling FA. (1975). Glutamine synthetase forms three- and seven-stranded helical cables.Proc. Natl. Acad. Sci. U.S.A.. Sep 1975. 72(9):3402-6. [Abstract]
  • Scanlon WJ, Eisenberg D. (1975). Solvation of crystalline proteins: theory and its application to available data.J. Mol. Biol.. Nov 1975. 98(3):485-502. [Abstract]

1972

1971

  • Heidner EG, Weber BH, Eisenberg D. (1971). Subunit structure of aldolase.Science. Feb 1971. 171(3972):677-9. [Abstract]
  • Dickerson RE, Takano T, Eisenberg D, Kallai OB, Samson L, Cooper A, Margoliash E. (1971). Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 A resolution.J. Biol. Chem.. Mar 1971. 246(5):1511-35. [Abstract]

1969

1967

Other

  • Rokito AS, Zuckerman JD, Shaari JM, Eisenberg DP, Cuomo F, Gallagher MA. (Other). A comparison of nonoperative and operative treatment of type II distal clavicle fractures.Bull Hosp Jt Dis. . 61(1-2):32-9. [Abstract]