David Eisenberg*
Publications:
Eisenberg D, Hou K, Ge P, Sawaya M, Dolinsky J, Yang Y, Jiang YX, Lutter L, Boyer D, Cheng X, Pi J, Zhang J, Lu J, Yang S, Yu Z, Feigon J. How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer's disease brain by a strain-relief mechanism. Res Sq. 2024 May 08. view on PubMed
Hou K, Pan H, Shahpasand-Kroner H, Hu C, Abskharon R, Seidler P, Mekkittikul M, Balbirnie M, Lantz C, Sawaya MR, Dolinsky JL, Jones M, Zuo X, Loo JA, Frautschy S, Cole G, Eisenberg DS. D-peptide-magnetic nanoparticles fragment tau fibrils and rescue behavioral deficits in a mouse model of Alzheimer's disease. Sci Adv. 2024 May 03; 10(18):eadl2991. view on PubMed
Hou K, Ge P, Sawaya MR, Dolinsky JL, Yang Y, Jiang YX, Lutter L, Boyer DR, Cheng X, Pi J, Zhang J, Lu J, Yang S, Yu Z, Feigon J, Eisenberg DS. How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer's disease brain by a strain-relief mechanism. bioRxiv. 2024 Mar 29. view on PubMed
Ryder BD, Ustyantseva E, Boyer DR, Mendoza-Oliva A, Kuska M, Wydorski PM, Macierzynska P, Morgan N, Sawaya MR, Diamond MI, Kampinga HH, Joachimiak L. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity. bioRxiv. 2024 Jan 23. view on PubMed
Nguyen BA, Singh V, Afrin S, Yakubovska A, Wang L, Ahmed Y, Pedretti R, Fernandez-Ramirez MDC, Singh P, Pekala M, Cabrera Hernandez LO, Kumar S, Lemoff A, Gonzalez-Prieto R, Sawaya MR, Eisenberg DS, Benson MD, Saelices L. Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy. Nat Commun. 2024 Jan 17; 15(1):581. view on PubMed
Lu J, Ge P, Sawaya MR, Hughes MP, Boyer DR, Cao Q, Abskharon R, Cascio D, Tayeb-Fligelman E, Eisenberg DS. Cryo-EM structures of the D290V mutant of the hnRNPA2 low-complexity domain suggests how D290V affects phase separation and aggregation. J Biol Chem. 2024 Feb; 300(2):105531. view on PubMed
Rosenberg GM, Abskharon R, Boyer DR, Ge P, Sawaya MR, Eisenberg DS. Fibril structures of TFG protein mutants validate the identification of TFG as a disease-related amyloid protein by the IMPAcT method. PNAS Nexus. 2023 Dec; 2(12):pgad402. view on PubMed
Hazari A, Sawaya MR, Sajimon M, Vlahakis N, Rodriguez J, Eisenberg D, Raskatov JA. Racemic Peptides from Amyloid β and Amylin Form Rippled β-Sheets Rather Than Pleated β-Sheets. J Am Chem Soc. 2023 11 29; 145(47):25917-25926. view on PubMed
Abskharon R, Pan H, Sawaya MR, Seidler PM, Olivares EJ, Chen Y, Murray KA, Zhang J, Lantz C, Bentzel M, Boyer DR, Cascio D, Nguyen BA, Hou K, Cheng X, Pardon E, Williams CK, Nana AL, Vinters HV, Spina S, Grinberg LT, Seeley WW, Steyaert J, Glabe CG, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Structure-based design of nanobodies that inhibit seeding of Alzheimer's patient-extracted tau fibrils. Proc Natl Acad Sci U S A. 2023 10 10; 120(41):e2300258120. view on PubMed
Samelson AJ, Ariqat N, McKetney J, Rohanitazangi G, Bravo CP, Goodness D, Tian R, Grosjean P, Abskharon R, Eisenberg D, Kanaan NM, Gan L, Condello C, Swaney DL, Kampmann M. CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis. bioRxiv. 2023 Jun 26. view on PubMed
Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. Nat Commun. 2023 04 25; 14(1):2379. view on PubMed
Murray KA, Hu CJ, Pan H, Lu J, Abskharon R, Bowler JT, Rosenberg GM, Williams CK, Elezi G, Balbirnie M, Faull KF, Vinters HV, Seidler PM, Eisenberg DS. Small molecules disaggregate alpha-synuclein and prevent seeding from patient brain-derived fibrils. Proc Natl Acad Sci U S A. 2023 02 14; 120(7):e2217835120. view on PubMed
Buxbaum JN, Dispenzieri A, Eisenberg DS, Fändrich M, Merlini G, Saraiva MJM, Sekijima Y, Westermark P. Amyloid nomenclature 2022: update, novel proteins, and recommendations by the International Society of Amyloidosis (ISA) Nomenclature Committee. Amyloid. 2022 Dec; 29(4):213-219. view on PubMed
Seidler PM, Murray KA, Boyer DR, Ge P, Sawaya MR, Hu CJ, Cheng X, Abskharon R, Pan H, DeTure MA, Williams CK, Dickson DW, Vinters HV, Eisenberg DS. Structure-based discovery of small molecules that disaggregate Alzheimer's disease tissue derived tau fibrils in vitro. Nat Commun. 2022 09 16; 13(1):5451. view on PubMed
Bowler JT, Sawaya MR, Boyer DR, Cascio D, Bali M, Eisenberg DS. Micro-electron diffraction structure of the aggregation-driving N terminus of Drosophila neuronal protein Orb2A reveals amyloid-like β-sheets. J Biol Chem. 2022 10; 298(10):102396. view on PubMed
Murray KA, Hu CJ, Griner SL, Pan H, Bowler JT, Abskharon R, Rosenberg GM, Cheng X, Seidler PM, Eisenberg DS. De novo designed protein inhibitors of amyloid aggregation and seeding. Proc Natl Acad Sci U S A. 2022 08 23; 119(34):e2206240119. view on PubMed
Hazari A, Sawaya MR, Vlahakis N, Johnstone TC, Boyer D, Rodriguez J, Eisenberg D, Raskatov JA. The rippled β-sheet layer configuration-a novel supramolecular architecture based on predictions by Pauling and Corey. Chem Sci. 2022 Aug 10; 13(31):8947-8952. view on PubMed
Murray KA, Hughes MP, Hu CJ, Sawaya MR, Salwinski L, Pan H, French SW, Seidler PM, Eisenberg DS. Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies. Nat Struct Mol Biol. 2022 06; 29(6):529-536. view on PubMed
Rosenberg GM, Murray KA, Salwinski L, Hughes MP, Abskharon R, Eisenberg DS. Bioinformatic identification of previously unrecognized amyloidogenic proteins. J Biol Chem. 2022 05; 298(5):101920. view on PubMed
Abskharon R, Sawaya MR, Boyer DR, Cao Q, Nguyen BA, Cascio D, Eisenberg DS. Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation. Proc Natl Acad Sci U S A. 2022 04 12; 119(15):e2119952119. view on PubMed
Jiang YX, Cao Q, Sawaya MR, Abskharon R, Ge P, DeTure M, Dickson DW, Fu JY, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Amyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43. Nature. 2022 05; 605(7909):304-309. view on PubMed
Murray KA, Evans D, Hughes MP, Sawaya MR, Hu CJ, Houk KN, Eisenberg D. Extended β-Strands Contribute to Reversible Amyloid Formation. ACS Nano. 2022 02 22; 16(2):2154-2163. view on PubMed
Gray ALH, Sawaya MR, Acharyya D, Lou J, Edington EM, Best MD, Prosser RA, Eisenberg DS, Do TD. Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices. Protein Sci. 2022 03; 31(3):716-727. view on PubMed
Hughes MP, Goldschmidt L, Eisenberg DS. Prevalence and species distribution of the low-complexity, amyloid-like, reversible, kinked segment structural motif in amyloid-like fibrils. J Biol Chem. 2021 10; 297(4):101194. view on PubMed
Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis. Cell. 2021 09 16; 184(19):4857-4873. view on PubMed
Cao Q, Boyer DR, Sawaya MR, Abskharon R, Saelices L, Nguyen BA, Lu J, Murray KA, Kandeel F, Eisenberg DS. Cryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril cores. Nat Struct Mol Biol. 2021 09; 28(9):724-730. view on PubMed
Tayeb-Fligelman E, Cheng X, Tai C, Bowler JT, Griner S, Sawaya MR, Seidler PM, Jiang YX, Lu J, Rosenberg GM, Salwinski L, Abskharon R, Zee CT, Hou K, Li Y, Boyer DR, Murray KA, Falcon G, Anderson DH, Cascio D, Saelices L, Damoiseaux R, Guo F, Eisenberg DS. Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2. bioRxiv. 2021 Mar 18. view on PubMed
Shipps C, Kelly HR, Dahl PJ, Yi SM, Vu D, Boyer D, Glynn C, Sawaya MR, Eisenberg D, Batista VS, Malvankar NS. Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines. Proc Natl Acad Sci U S A. 2021 01 12; 118(2). view on PubMed
Benson MD, Buxbaum JN, Eisenberg DS, Merlini G, Saraiva MJM, Sekijima Y, Sipe JD, Westermark P. Amyloid nomenclature 2020: update and recommendations by the International Society of Amyloidosis (ISA) nomenclature committee. Amyloid. 2020 Dec; 27(4):217-222. view on PubMed
Lu J, Cao Q, Hughes MP, Sawaya MR, Boyer DR, Cascio D, Eisenberg DS. CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid. Nat Commun. 2020 08 14; 11(1):4090. view on PubMed
Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev. 2020 Aug 07; 49(15):5473-5509. view on PubMed
Cao Q, Boyer DR, Sawaya MR, Ge P, Eisenberg DS. Cryo-EM structure and inhibitor design of human IAPP (amylin) fibrils. Nat Struct Mol Biol. 2020 07; 27(7):653-659. view on PubMed
Abskharon R, Seidler PM, Sawaya MR, Cascio D, Yang TP, Philipp S, Williams CK, Newell KL, Ghetti B, DeTure MA, Dickson DW, Vinters HV, Felgner PL, Nakajima R, Glabe CG, Eisenberg DS. Crystal structure of a conformational antibody that binds tau oligomers and inhibits pathological seeding by extracts from donors with Alzheimer's disease. J Biol Chem. 2020 07 31; 295(31):10662-10676. view on PubMed
Glynn C, Sawaya MR, Ge P, Gallagher-Jones M, Short CW, Bowman R, Apostol M, Zhou ZH, Eisenberg DS, Rodriguez JA. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Nat Struct Mol Biol. 2020 05; 27(5):417-423. view on PubMed
Boyer DR, Li B, Sun C, Fan W, Zhou K, Hughes MP, Sawaya MR, Jiang L, Eisenberg DS. The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure. Proc Natl Acad Sci U S A. 2020 02 18; 117(7):3592-3602. view on PubMed
Sangwan S, Sahay S, Murray KA, Morgan S, Guenther EL, Jiang L, Williams CK, Vinters HV, Goedert M, Eisenberg DS. Inhibition of synucleinopathic seeding by rationally designed inhibitors. Elife. 2020 01 02; 9. view on PubMed
Basavalingappa V, Bera S, Xue B, Azuri I, Tang Y, Tao K, Shimon LJW, Sawaya MR, Kolusheva S, Eisenberg DS, Kronik L, Cao Y, Wei G, Gazit E. Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid. Nat Commun. 2019 11 20; 10(1):5256. view on PubMed
Boyer DR, Li B, Sun C, Fan W, Sawaya MR, Jiang L, Eisenberg DS. Structures of fibrils formed by α-synuclein hereditary disease mutant H50Q reveal new polymorphs. Nat Struct Mol Biol. 2019 11; 26(11):1044-1052. view on PubMed
Griner SL, Seidler P, Bowler J, Murray KA, Yang TP, Sahay S, Sawaya MR, Cascio D, Rodriguez JA, Philipp S, Sosna J, Glabe CG, Gonen T, Eisenberg DS. Structure-based inhibitors of amyloid beta core suggest a common interface with tau. Elife. 2019 10 15; 8. view on PubMed
Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Author Correction: Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation. Nat Struct Mol Biol. 2019 Oct; 26(10):988. view on PubMed
Makam P, Yamijala SSRKC, Tao K, Shimon LJW, Eisenberg DS, Sawaya MR, Wong BM, Gazit E. Non-proteinaceous hydrolase comprised of a phenylalanine metallo-supramolecular amyloid-like structure. Nat Catal. 2019 Nov; 2(11):977-985. view on PubMed
Seidler PM, Boyer DR, Murray KA, Yang TP, Bentzel M, Sawaya MR, Rosenberg G, Cascio D, Williams CK, Newell KL, Ghetti B, DeTure MA, Dickson DW, Vinters HV, Eisenberg DS. Structure-based inhibitors halt prion-like seeding by Alzheimer's disease-and tauopathy-derived brain tissue samples. J Biol Chem. 2019 11 01; 294(44):16451-16464. view on PubMed
Warmack RA, Boyer DR, Zee CT, Richards LS, Sawaya MR, Cascio D, Gonen T, Eisenberg DS, Clarke SG. Structure of amyloid-β (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface. Nat Commun. 2019 07 26; 10(1):3357. view on PubMed
Cao Q, Boyer DR, Sawaya MR, Ge P, Eisenberg DS. Cryo-EM structures of four polymorphic TDP-43 amyloid cores. Nat Struct Mol Biol. 2019 07; 26(7):619-627. view on PubMed
Lu J, Cao Q, Wang C, Zheng J, Luo F, Xie J, Li Y, Ma X, He L, Eisenberg D, Nowick J, Jiang L, Li D. Structure-Based Peptide Inhibitor Design of Amyloid-β Aggregation. Front Mol Neurosci. 2019; 12:54. view on PubMed
Saelices L, Nguyen BA, Chung K, Wang Y, Ortega A, Lee JH, Coelho T, Bijzet J, Benson MD, Eisenberg DS. A pair of peptides inhibits seeding of the hormone transporter transthyretin into amyloid fibrils. J Biol Chem. 2019 04 12; 294(15):6130-6141. view on PubMed
Benson MD, Buxbaum JN, Eisenberg DS, Merlini G, Saraiva MJM, Sekijima Y, Sipe JD, Westermark P. Amyloid nomenclature 2018: recommendations by the International Society of Amyloidosis (ISA) nomenclature committee. Amyloid. 2018 Dec; 25(4):215-219. view on PubMed
Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. Author Correction: Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem. 2018 12; 10(12):1267. view on PubMed
Tuukkanen AT, Freire D, Chan S, Arbing MA, Reed RW, Evans TJ, Zenkeviciute G, Kim J, Kahng S, Sawaya MR, Chaton CT, Wilmanns M, Eisenberg D, Parret AHA, Korotkov KV. Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems. J Mol Biol. 2019 01 18; 431(2):289-307. view on PubMed
Vogler TO, Wheeler JR, Nguyen ED, Hughes MP, Britson KA, Lester E, Rao B, Betta ND, Whitney ON, Ewachiw TE, Gomes E, Shorter J, Lloyd TE, Eisenberg DS, Taylor JP, Johnson AM, Olwin BB, Parker R. TDP-43 and RNA form amyloid-like myo-granules in regenerating muscle. Nature. 2018 11; 563(7732):508-513. view on PubMed
Brumshtein B, Esswein SR, Sawaya MR, Rosenberg G, Ly AT, Landau M, Eisenberg DS. Identification of two principal amyloid-driving segments in variable domains of Ig light chains in systemic light-chain amyloidosis. J Biol Chem. 2018 12 21; 293(51):19659-19671. view on PubMed
Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design. Nat Chem. 2018 12; 10(12):1213-1221. view on PubMed
Saelices L, Pokrzywa M, Pawelek K, Eisenberg DS. Assessment of the effects of transthyretin peptide inhibitors in Drosophila models of neuropathic ATTR. Neurobiol Dis. 2018 12; 120:118-125. view on PubMed
Li B, Ge P, Murray KA, Sheth P, Zhang M, Nair G, Sawaya MR, Shin WS, Boyer DR, Ye S, Eisenberg DS, Zhou ZH, Jiang L. Cryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernel. Nat Commun. 2018 09 06; 9(1):3609. view on PubMed
McPartland L, Heller DM, Eisenberg DS, Hochschild A, Sawaya MR. Atomic insights into the genesis of cellular filaments by globular proteins. Nat Struct Mol Biol. 2018 08; 25(8):705-714. view on PubMed
Eisenberg DS. Paul D. Boyer (1918-2018). Science. 2018 Jul 27; 361(6400):334. view on PubMed
Saelices L, Chung K, Lee JH, Cohn W, Whitelegge JP, Benson MD, Eisenberg DS. Amyloid seeding of transthyretin by ex vivo cardiac fibrils and its inhibition. Proc Natl Acad Sci U S A. 2018 07 17; 115(29):E6741-E6750. view on PubMed
Eisenberg DS. How Hard It Is Seeing What Is in Front of Your Eyes. Cell. 2018 06 28; 174(1):8-11. view on PubMed
Saelices L, Sievers SA, Sawaya MR, Eisenberg DS. Crystal structures of amyloidogenic segments of human transthyretin. Protein Sci. 2018 07; 27(7):1295-1303. view on PubMed
Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation. Nat Struct Mol Biol. 2018 06; 25(6):463-471. view on PubMed
Guenther EL, Ge P, Trinh H, Sawaya MR, Cascio D, Boyer DR, Gonen T, Zhou ZH, Eisenberg DS. Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2. Nat Struct Mol Biol. 2018 04; 25(4):311-319. view on PubMed
Sangwan S, Sawaya MR, Murray KA, Hughes MP, Eisenberg DS. Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations. Protein Sci. 2018 07; 27(7):1231-1242. view on PubMed
Do TD, Sangwan S, de Almeida NEC, Ilitchev AI, Giammona M, Sawaya MR, Buratto SK, Eisenberg DS, Bowers MT. Distal amyloid β-protein fragments template amyloid assembly. Protein Sci. 2018 07; 27(7):1181-1190. view on PubMed
Hughes MP, Sawaya MR, Boyer DR, Goldschmidt L, Rodriguez JA, Cascio D, Chong L, Gonen T, Eisenberg DS. Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks. Science. 2018 02 09; 359(6376):698-701. view on PubMed
Gallagher-Jones M, Glynn C, Boyer DR, Martynowycz MW, Hernandez E, Miao J, Zee CT, Novikova IV, Goldschmidt L, McFarlane HT, Helguera GF, Evans JE, Sawaya MR, Cascio D, Eisenberg DS, Gonen T, Rodriguez JA. Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp. Nat Struct Mol Biol. 2018 02; 25(2):131-134. view on PubMed
Hanczyc P, Mikhailovsky A, Boyer DR, Sawaya MR, Heeger A, Eisenberg D. Ultrafast Time-Resolved Studies on Fluorescein for Recognition Strands Architecture in Amyloid Fibrils. J Phys Chem B. 2018 01 11; 122(1):8-18. view on PubMed
Krotee P, Griner SL, Sawaya MR, Cascio D, Rodriguez JA, Shi D, Philipp S, Murray K, Saelices L, Lee J, Seidler P, Glabe CG, Jiang L, Gonen T, Eisenberg DS. Common fibrillar spines of amyloid-β and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors. J Biol Chem. 2018 02 23; 293(8):2888-2902. view on PubMed
Kurt TD, Aguilar-Calvo P, Jiang L, Rodriguez JA, Alderson N, Eisenberg DS, Sigurdson CJ. Asparagine and glutamine ladders promote cross-species prion conversion. J Biol Chem. 2017 11 17; 292(46):19076-19086. view on PubMed
Rodriguez JA, Jiang L, Eisenberg DS. Toward the Atomic Structure of PrPSc. Cold Spring Harb Perspect Biol. 2017 Sep 01; 9(9). view on PubMed
Sangwan S, Zhao A, Adams KL, Jayson CK, Sawaya MR, Guenther EL, Pan AC, Ngo J, Moore DM, Soriaga AB, Do TD, Goldschmidt L, Nelson R, Bowers MT, Koehler CM, Shaw DE, Novitch BG, Eisenberg DS. Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS). Proc Natl Acad Sci U S A. 2017 08 15; 114(33):8770-8775. view on PubMed
Goedert M, Eisenberg DS, Crowther RA. Propagation of Tau Aggregates and Neurodegeneration. Annu Rev Neurosci. 2017 07 25; 40:189-210. view on PubMed
Eisenberg DS, Sawaya MR. Neurodegeneration: Taming tangled tau. Nature. 2017 07 13; 547(7662):170-171. view on PubMed
Rodriguez JA, Eisenberg DS, Gonen T. Taking the measure of MicroED. Curr Opin Struct Biol. 2017 10; 46:79-86. view on PubMed
Popp D, Loh ND, Zorgati H, Ghoshdastider U, Liow LT, Ivanova MI, Larsson M, DePonte DP, Bean R, Beyerlein KR, Gati C, Oberthuer D, Arnlund D, Brändén G, Berntsen P, Cascio D, Chavas LMG, Chen JPJ, Ding K, Fleckenstein H, Gumprecht L, Harimoorthy R, Mossou E, Sawaya MR, Brewster AS, Hattne J, Sauter NK, Seibert M, Seuring C, Stellato F, Tilp T, Eisenberg DS, Messerschmidt M, Williams GJ, Koglin JE, Makowski L, Millane RP, Forsyth T, Boutet S, White TA, Barty A, Chapman H, Chen SL, Liang M, Neutze R, Robinson RC. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Cytoskeleton (Hoboken). 2017 Dec; 74(12):472-481. view on PubMed
de la Cruz MJ, Hattne J, Shi D, Seidler P, Rodriguez J, Reyes FE, Sawaya MR, Cascio D, Weiss SC, Kim SK, Hinck CS, Hinck AP, Calero G, Eisenberg D, Gonen T. Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. Nat Methods. 2017 Feb 13; 14(4):399-402. view on PubMed
Buchner J, Eisenberg D, Schmid F. In memoriam-Rainer Jaenicke. Protein Sci. 2017 03; 26(3):394-395. view on PubMed
Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Philipp S, Griner S, Jiang L, Glabe CG, Westermark GT, Gonen T, Eisenberg DS. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity. Elife. 2017 01 03; 6. view on PubMed
Eisenberg DS, Sawaya MR. Structural Studies of Amyloid Proteins at the Molecular Level. Annu Rev Biochem. 2017 06 20; 86:69-95. view on PubMed
Riek R, Eisenberg DS. The activities of amyloids from a structural perspective. Nature. 2016 11 10; 539(7628):227-235. view on PubMed
Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature. 2016 11 03; 539(7627):43-47. view on PubMed
Sawaya MR, Rodriguez J, Cascio D, Collazo MJ, Shi D, Reyes FE, Hattne J, Gonen T, Eisenberg DS. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED. Proc Natl Acad Sci U S A. 2016 10 04; 113(40):11232-11236. view on PubMed
Eisenberg DS, Sawaya MR. Implications for Alzheimer's disease of an atomic resolution structure of amyloid-β(1-42) fibrils. Proc Natl Acad Sci U S A. 2016 08 23; 113(34):9398-400. view on PubMed
Wagner JM, Chan S, Evans TJ, Kahng S, Kim J, Arbing MA, Eisenberg D, Korotkov KV. Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. BMC Struct Biol. 2016 Feb 27; 16:5. view on PubMed
Soriaga AB, Sangwan S, Macdonald R, Sawaya MR, Eisenberg D. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets. J Phys Chem B. 2016 07 07; 120(26):5810-6. view on PubMed
Do TD, LaPointe NE, Nelson R, Krotee P, Hayden EY, Ulrich B, Quan S, Feinstein SC, Teplow DB, Eisenberg D, Shea JE, Bowers MT. Amyloid β-Protein C-Terminal Fragments: Formation of Cylindrins and β-Barrels. J Am Chem Soc. 2016 Jan 20; 138(2):549-57. view on PubMed
Sangwan S, Eisenberg DS. Perspective on SOD1 mediated toxicity in Amyotrophic Lateral Sclerosis. Postepy Biochem. 2016; 62(3):362-369. view on PubMed
Moshe A, Landau M, Eisenberg D. Preparation of Crystalline Samples of Amyloid Fibrils and Oligomers. Methods Mol Biol. 2016; 1345:201-10. view on PubMed
Soragni A, Janzen DM, Johnson LM, Lindgren AG, Thai-Quynh Nguyen A, Tiourin E, Soriaga AB, Lu J, Jiang L, Faull KF, Pellegrini M, Memarzadeh S, Eisenberg DS. A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer Cell. 2016 Jan 11; 29(1):90-103. view on PubMed
Yin JX, Maalouf M, Han P, Zhao M, Gao M, Dharshaun T, Ryan C, Whitelegge J, Wu J, Eisenberg D, Reiman EM, Schweizer FE, Shi J. Ketones block amyloid entry and improve cognition in an Alzheimer's model. Neurobiol Aging. 2016 Mar; 39:25-37. view on PubMed
Brumshtein B, Esswein SR, Salwinski L, Phillips ML, Ly AT, Cascio D, Sawaya MR, Eisenberg DS. Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain. Elife. 2015 Nov 18; 4:e10935. view on PubMed
Saelices L, Johnson LM, Liang WY, Sawaya MR, Cascio D, Ruchala P, Whitelegge J, Jiang L, Riek R, Eisenberg DS. Uncovering the Mechanism of Aggregation of Human Transthyretin. J Biol Chem. 2015 Nov 27; 290(48):28932-43. view on PubMed
Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS. Structure of the toxic core of α-synuclein from invisible crystals. Nature. 2015 Sep 24; 525(7570):486-90. view on PubMed
Kurt TD, Jiang L, Fernández-Borges N, Bett C, Liu J, Yang T, Spraker TR, Castilla J, Eisenberg D, Kong Q, Sigurdson CJ. Human prion protein sequence elements impede cross-species chronic wasting disease transmission. J Clin Invest. 2015 Jun; 125(6):2548. view on PubMed
Soragni A, Yousefi S, Stoeckle C, Soriaga AB, Sawaya MR, Kozlowski E, Schmid I, Radonjic-Hoesli S, Boutet S, Williams GJ, Messerschmidt M, Seibert MM, Cascio D, Zatsepin NA, Burghammer M, Riekel C, Colletier JP, Riek R, Eisenberg DS, Simon HU. Toxicity of eosinophil MBP is repressed by intracellular crystallization and promoted by extracellular aggregation. Mol Cell. 2015 Mar 19; 57(6):1011-1021. view on PubMed
Kurt TD, Jiang L, Fernández-Borges N, Bett C, Liu J, Yang T, Spraker TR, Castilla J, Eisenberg D, Kong Q, Sigurdson CJ. Human prion protein sequence elements impede cross-species chronic wasting disease transmission. J Clin Invest. 2015 Apr; 125(4):1485-96. view on PubMed
Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Acta Crystallogr D Biol Crystallogr. 2015 Feb; 71(Pt 2):357-66. view on PubMed
Li D, Jones EM, Sawaya MR, Furukawa H, Luo F, Ivanova M, Sievers SA, Wang W, Yaghi OM, Liu C, Eisenberg DS. Structure-based design of functional amyloid materials. J Am Chem Soc. 2014 Dec 31; 136(52):18044-51. view on PubMed
Eisenberg D, Ahn HS, Bard AJ. Enhanced photoelectrochemical water oxidation on bismuth vanadate by electrodeposition of amorphous titanium dioxide. J Am Chem Soc. 2014 Oct 08; 136(40):14011-4. view on PubMed
Brumshtein B, Esswein SR, Landau M, Ryan CM, Whitelegge JP, Phillips ML, Cascio D, Sawaya MR, Eisenberg DS. Formation of amyloid fibers by monomeric light chain variable domains. J Biol Chem. 2014 Oct 03; 289(40):27513-25. view on PubMed
Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier JP, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park HW, Federici BA, Sauter NK, Schlichting I, Eisenberg DS. Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proc Natl Acad Sci U S A. 2014 Sep 02; 111(35):12769-74. view on PubMed
Do TD, LaPointe NE, Sangwan S, Teplow DB, Feinstein SC, Sawaya MR, Eisenberg DS, Bowers MT. Factors that drive peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants. J Phys Chem B. 2014 Jul 03; 118(26):7247-56. view on PubMed
Hochberg GK, Ecroyd H, Liu C, Cox D, Cascio D, Sawaya MR, Collier MP, Stroud J, Carver JA, Baldwin AJ, Robinson CV, Eisenberg DS, Benesch JL, Laganowsky A. The structured core domain of αB-crystallin can prevent amyloid fibrillation and associated toxicity. Proc Natl Acad Sci U S A. 2014 Apr 22; 111(16):E1562-70. view on PubMed
Korman TP, Sahachartsiri B, Li D, Vinokur JM, Eisenberg D, Bowie JU. A synthetic biochemistry system for the in vitro production of isoprene from glycolysis intermediates. Protein Sci. 2014 May; 23(5):576-85. view on PubMed
Kurt TD, Jiang L, Bett C, Eisenberg D, Sigurdson CJ. A proposed mechanism for the promotion of prion conversion involving a strictly conserved tyrosine residue in the β2-α2 loop of PrPC. J Biol Chem. 2014 Apr 11; 289(15):10660-10667. view on PubMed
Goldschmidt L, Eisenberg D, Derewenda ZS. Salvage or recovery of failed targets by mutagenesis to reduce surface entropy. Methods Mol Biol. 2014; 1140:201-9. view on PubMed
Li D, Furukawa H, Deng H, Liu C, Yaghi OM, Eisenberg DS. Designed amyloid fibers as materials for selective carbon dioxide capture. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):191-6. view on PubMed
Ivanova MI, Sievers SA, Guenther EL, Johnson LM, Winkler DD, Galaleldeen A, Sawaya MR, Hart PJ, Eisenberg DS. Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):197-201. view on PubMed
Arbing MA, Chan S, Harris L, Kuo E, Zhou TT, Ahn CJ, Nguyen L, He Q, Lu J, Menchavez PT, Shin A, Holton T, Sawaya MR, Cascio D, Eisenberg D. Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions. PLoS One. 2013; 8(11):e81753. view on PubMed
Jiang L, Liu C, Leibly D, Landau M, Zhao M, Hughes MP, Eisenberg DS. Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta. Elife. 2013 Jul 16; 2:e00857. view on PubMed
Miallau L, Jain P, Arbing MA, Cascio D, Phan T, Ahn CJ, Chan S, Chernishof I, Maxson M, Chiang J, Jacobs WR, Eisenberg DS. Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes. Structure. 2013 Apr 02; 21(4):627-37. view on PubMed
Liu C, Zhao M, Jiang L, Cheng PN, Park J, Sawaya MR, Pensalfini A, Gou D, Berk AJ, Glabe CG, Nowick J, Eisenberg D. Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates. Proc Natl Acad Sci U S A. 2012 Dec 18; 109(51):20913-8. view on PubMed
Min AB, Miallau L, Sawaya MR, Habel J, Cascio D, Eisenberg D. 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 Sci. 2012 Nov; 21(11):1754-67. view on PubMed
Cheng PN, Liu C, Zhao M, Eisenberg D, Nowick JS. Amyloid β-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity. Nat Chem. 2012 Nov; 4(11):927-33. view on PubMed
Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin NV, Frantz DE, Schneider JW, Chen S, Li L, Sawaya MR, Eisenberg D, Tycko R, McKnight SL. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell. 2012 May 11; 149(4):753-67. view on PubMed
Stroud JC, Liu C, Teng PK, Eisenberg D. Toxic fibrillar oligomers of amyloid-β have cross-β structure. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):7717-22. view on PubMed
Eisenberg D, Jucker M. The amyloid state of proteins in human diseases. Cell. 2012 Mar 16; 148(6):1188-203. view on PubMed
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Teng PK, Anderson NJ, Goldschmidt L, Sawaya MR, Sambashivan S, Eisenberg D. Ribonuclease A suggests how proteins self-chaperone against amyloid fiber formation. Protein Sci. 2012 Jan; 21(1):26-37. view on PubMed
Colletier JP, Laganowsky A, Landau M, Zhao M, Soriaga AB, Goldschmidt L, Flot D, Cascio D, Sawaya MR, Eisenberg D. Molecular basis for amyloid-beta polymorphism. Proc Natl Acad Sci U S A. 2011 Oct 11; 108(41):16938-43. view on PubMed
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun 29; 8(7):528-9. view on PubMed
Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. 2011 Jun 15; 475(7354):96-100. view on PubMed
Landau M, Sawaya MR, Faull KF, Laganowsky A, Jiang L, Sievers SA, Liu J, Barrio JR, Eisenberg D. Towards a pharmacophore for amyloid. PLoS Biol. 2011 Jun; 9(6):e1001080. view on PubMed
Zhao M, Cascio D, Sawaya MR, Eisenberg D. Structures of segments of α-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation. Protein Sci. 2011 Jun; 20(6):996-1004. view on PubMed
Liu C, Sawaya MR, Cheng PN, Zheng J, Nowick JS, Eisenberg D. Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic β-sheet mimics. J Am Chem Soc. 2011 May 04; 133(17):6736-44. view on PubMed
Apostol MI, Wiltzius JJ, Sawaya MR, Cascio D, Eisenberg D. Atomic structures suggest determinants of transmission barriers in mammalian prion disease. Biochemistry. 2011 Apr 05; 50(13):2456-63. view on PubMed
Zheng J, Liu C, Sawaya MR, Vadla B, Khan S, Woods RJ, Eisenberg D, Goux WJ, Nowick JS. Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide. J Am Chem Soc. 2011 Mar 09; 133(9):3144-57. view on PubMed
Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MN, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb). 2011 Mar; 91(2):155-72. view on PubMed
Liu C, Sawaya MR, Eisenberg D. β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages. Nat Struct Mol Biol. 2011 Jan; 18(1):49-55. view on PubMed
Arbing MA, Kaufmann M, Phan T, Chan S, Cascio D, Eisenberg D. The crystal structure of the Mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer. Protein Sci. 2010 Sep; 19(9):1692-703. view on PubMed
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 Aug 25; 132(33):11622-8. view on PubMed
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 Sep 24; 285(39):29671-5. view on PubMed
Eisenberg D, Shenhar R, Rabinovitz M. Synthetic approaches to aromatic belts: building up strain in macrocyclic polyarenes. Chem Soc Rev. 2010 Aug; 39(8):2879-90. view on PubMed
Ostapchenko VG, Sawaya MR, Makarava N, Savtchenko R, Nilsson KP, Eisenberg D, Baskakov IV. Two amyloid States of the prion protein display significantly different folding patterns. J Mol Biol. 2010 Jul 23; 400(4):908-21. view on PubMed
Wang L, Schubert D, Sawaya MR, Eisenberg D, Riek R. Multidimensional structure-activity relationship of a protein in its aggregated states. Angew Chem Int Ed Engl. 2010 May 25; 49(23):3904-8. view on PubMed
Laganowsky A, Benesch JL, Landau M, Ding L, Sawaya MR, Cascio D, Huang Q, Robinson CV, Horwitz J, Eisenberg D. Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function. Protein Sci. 2010 May; 19(5):1031-43. view on PubMed
Goldschmidt L, Teng PK, Riek R, Eisenberg D. Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3487-92. view on PubMed
Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009 Dec 14; 3:115. view on PubMed
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. Recurated protein interaction datasets. Nat Methods. 2009 Dec; 6(12):860-1. view on PubMed
Ivanova MI, Sievers SA, Sawaya MR, Wall JS, Eisenberg D. Molecular basis for insulin fibril assembly. Proc Natl Acad Sci U S A. 2009 Nov 10; 106(45):18990-5. view on PubMed
Wiltzius JJ, Landau M, Nelson R, Sawaya MR, Apostol MI, Goldschmidt L, Soriaga AB, Cascio D, Rajashankar K, Eisenberg D. Molecular mechanisms for protein-encoded inheritance. Nat Struct Mol Biol. 2009 Sep; 16(9):973-8. view on PubMed
Teng PK, Eisenberg D. Short protein segments can drive a non-fibrillizing protein into the amyloid state. Protein Eng Des Sel. 2009 Aug; 22(8):531-6. view on PubMed
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 Sci. 2009 Jul; 18(7):1521-30. view on PubMed
Maji SK, Perrin MH, Sawaya MR, Jessberger S, Vadodaria K, Rissman RA, Singru PS, Nilsson KP, Simon R, Schubert D, Eisenberg D, Rivier J, Sawchenko P, Vale W, Riek R. Functional amyloids as natural storage of peptide hormones in pituitary secretory granules. Science. 2009 Jul 17; 325(5938):328-32. view on PubMed
Zhang K, Sawaya MR, Eisenberg DS, Liao JC. Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci U S A. 2008 Dec 30; 105(52):20653-8. view on PubMed
Llewellyn R, Eisenberg DS. Annotating proteins with generalized functional linkages. Proc Natl Acad Sci U S A. 2008 Nov 18; 105(46):17700-5. view on PubMed
Medrano-Soto A, Pal D, Eisenberg D. Inferring molecular function: contributions from functional linkages. Trends Genet. 2008 Dec; 24(12):587-90. view on PubMed
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 of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis. J Biol Chem. 2009 Jan 02; 284(1):276-283. view on PubMed
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 Sep 19; 134(6):1007-18. view on PubMed
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 Sep 12; 4(9):e1000174. view on PubMed
Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R. Bacterial inclusion bodies contain amyloid-like structure. PLoS Biol. 2008 Aug 05; 6(8):e195. view on PubMed
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. Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy. J Clin Invest. 2008 Aug; 118(8):2917-28. view on PubMed
Guo Z, Eisenberg D. The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold. Protein Sci. 2008 Sep; 17(9):1617-23. view on PubMed
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 (amylin). Protein Sci. 2008 Sep; 17(9):1467-74. view on PubMed
Miller CS, Eisenberg D. Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics. 2008 Jul 15; 24(14):1575-82. view on PubMed
Kuriyan J, Eisenberg D. The origin of protein interactions and allostery in colocalization. Nature. 2007 Dec 13; 450(7172):983-90. view on PubMed
Anderson DH, Kickhoefer VA, Sievers SA, Rome LH, Eisenberg D. Draft crystal structure of the vault shell at 9-A resolution. PLoS Biol. 2007 Nov; 5(11):e318. view on PubMed
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 09; 5:44. view on PubMed
Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D. Functional linkages can reveal protein complexes for structure determination. Structure. 2007 Sep; 15(9):1079-89. view on PubMed
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug; 25(8):894-8. view on PubMed
Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants. Protein Sci. 2007 Aug; 16(8):1569-76. view on PubMed
Salwinski L, Eisenberg D. The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. Bioinformatics. 2007 Aug 15; 23(16):2193-5. view on PubMed
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. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature. 2007 May 24; 447(7143):453-7. view on PubMed
Guo Z, Eisenberg D. The mechanism of the amyloidogenic conversion of T7 endonuclease I. J Biol Chem. 2007 May 18; 282(20):14968-74. view on PubMed
Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16. view on PubMed
Tsemekhman K, Goldschmidt L, Eisenberg D, Baker D. Cooperative hydrogen bonding in amyloid formation. Protein Sci. 2007 Apr; 16(4):761-4. view on PubMed
Strong M, Eisenberg D. The protein network as a tool for finding novel drug targets. Prog Drug Res. 2007; 64:191, 193-215. view on PubMed
White EL, Southworth K, Ross L, Cooley S, Gill RB, Sosa MI, Manouvakhova A, Rasmussen L, Goulding C, Eisenberg D, Fletcher TM. A novel inhibitor of Mycobacterium tuberculosis pantothenate synthetase. J Biomol Screen. 2007 Feb; 12(1):100-5. view on PubMed
Abdallah AM, Verboom T, Hannes F, Safi M, Strong M, Eisenberg D, Musters RJ, Vandenbroucke-Grauls CM, Appelmelk BJ, Luirink J, Bitter W. A specific secretion system mediates PPE41 transport in pathogenic mycobacteria. Mol Microbiol. 2006 Nov; 62(3):667-79. view on PubMed
Goulding CW, Bowers PM, Segelke B, Lekin T, Kim CY, Terwilliger TC, Eisenberg D. The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function. J Mol Biol. 2007 Jan 12; 365(2):275-83. view on PubMed
Eisenberg D, Nelson R, Sawaya MR, Balbirnie M, Sambashivan S, Ivanova MI, Madsen AØ, Riekel C. The structural biology of protein aggregation diseases: Fundamental questions and some answers. Acc Chem Res. 2006 Sep; 39(9):568-75. view on PubMed
Guo Z, Eisenberg D. Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I. Proc Natl Acad Sci U S A. 2006 May 23; 103(21):8042-7. view on PubMed
Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D. 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 May 23; 103(21):8060-5. view on PubMed
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Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. Bioinformatic challenges for the next decade(s). Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29; 361(1467):525-7. view on PubMed
Nelson R, Eisenberg D. Recent atomic models of amyloid fibril structure. Curr Opin Struct Biol. 2006 Apr; 16(2):260-5. view on PubMed
Ivanova MI, Thompson MJ, Eisenberg D. A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments. Proc Natl Acad Sci U S A. 2006 Mar 14; 103(11):4079-82. view on PubMed
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci U S A. 2006 Mar 14; 103(11):4074-8. view on PubMed
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. Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response. Science. 2006 Mar 24; 311(5768):1770-3. view on PubMed
Wang S, Eisenberg D. Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action. Biochemistry. 2006 Feb 14; 45(6):1554-61. view on PubMed
Rachman H, Strong M, Ulrichs T, Grode L, Schuchhardt J, Mollenkopf H, Kosmiadi GA, Eisenberg D, Kaufmann SH. Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. Infect Immun. 2006 Feb; 74(2):1233-42. view on PubMed
Rachman H, Strong M, Schaible U, Schuchhardt J, Hagens K, Mollenkopf H, Eisenberg D, Kaufmann SH. Mycobacterium tuberculosis gene expression profiling within the context of protein networks. Microbes Infect. 2006 Mar; 8(3):747-57. view on PubMed
Nelson R, Eisenberg D. Structural models of amyloid-like fibrils. Adv Protein Chem. 2006; 73:235-82. view on PubMed
Conboy L, Patel S, Kaptchuk TJ, Gottlieb B, Eisenberg D, Acevedo-Garcia D. Sociodemographic determinants of the utilization of specific types of complementary and alternative medicine: an analysis based on a nationally representative survey sample. J Altern Complement Med. 2005 Dec; 11(6):977-94. view on PubMed
Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D. Utilizing logical relationships in genomic data to decipher cellular processes. FEBS J. 2005 Oct; 272(20):5110-8. view on PubMed
Riley R, Lee C, Sabatti C, Eisenberg D. Inferring protein domain interactions from databases of interacting proteins. Genome Biol. 2005; 6(10):R89. view on PubMed
Sambashivan S, Liu Y, Sawaya MR, Gingery M, Eisenberg D. Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Nature. 2005 Sep 08; 437(7056):266-9. view on PubMed
Aprahamian I, Eisenberg D, Hoffman RE, Sternfeld T, Matsuo Y, Jackson EA, Nakamura E, Scott LT, Sheradsky T, Rabinovitz M. Ball-and-socket stacking of supercharged geodesic polyarenes: bonding by interstitial lithium ions. J Am Chem Soc. 2005 Jul 06; 127(26):9581-7. view on PubMed
Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature. 2005 Jun 09; 435(7043):773-8. view on PubMed
Li H, Sawaya MR, Tabita FR, Eisenberg D. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure. 2005 May; 13(5):779-89. view on PubMed
Goulding CW, Apostol MI, Sawaya MR, Phillips M, Parseghian A, Eisenberg D. Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme. J Mol Biol. 2005 May 27; 349(1):61-72. view on PubMed
Müller P, Sawaya MR, Pashkov I, Chan S, Nguyen C, Wu Y, Perry LJ, Eisenberg D. The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase. Acta Crystallogr D Biol Crystallogr. 2005 Mar; 61(Pt 3):309-15. view on PubMed
Li H, Pellegrini M, Eisenberg D. Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol. 2005 Feb; 23(2):253-60. view on PubMed
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Bowers PM, Cokus SJ, Eisenberg D, Yeates TO. Use of logic relationships to decipher protein network organization. Science. 2004 Dec 24; 306(5705):2246-9. view on PubMed
Reinhardt A, Eisenberg D. DPANN: improved sequence to structure alignments following fold recognition. Proteins. 2004 Aug 15; 56(3):528-38. view on PubMed
Bennett MJ, Eisenberg D. The evolving role of 3D domain swapping in proteins. Structure. 2004 Aug; 12(8):1339-41. view on PubMed
Ivanova MI, Sawaya MR, 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 Jul 20; 101(29):10584-9. view on PubMed
Salwinski L, Eisenberg D. In silico simulation of biological network dynamics. Nat Biotechnol. 2004 Aug; 22(8):1017-9. view on PubMed
Strong M, Cascio D, Eisenberg D. A web-based comparative genomics tutorial for investigating microbial genomes. Microbiol Educ. 2004 May; 5:30-5. view on PubMed
Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 2004; 5(5):R35. view on PubMed
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb; 22(2):177-83. view on PubMed
Kleiger G, Panina EM, Mallick P, Eisenberg D. PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence. Protein Sci. 2004 Jan; 13(1):221-9. view on PubMed
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D449-51. view on PubMed
Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, 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 Dec 15; 31(24):7099-109. view on PubMed
Lee S, Sawaya MR, Eisenberg D. 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. 2003 Dec; 59(Pt 12):2191-9. view on PubMed
Ivanova MI, Gingery M, Whitson LJ, Eisenberg D. Role of the C-terminal 28 residues of beta2-microglobulin in amyloid fibril formation. Biochemistry. 2003 Nov 25; 42(46):13536-40. view on PubMed
Goulding CW, Apostol MI, 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 Jan 30; 279(5):3516-24. view on PubMed
Hsu T, Hingley-Wilson SM, Chen B, Chen M, Dai AZ, Morin PM, Marks CB, Padiyar J, Goulding C, Gingery M, Eisenberg D, Russell RG, Derrick SC, Collins FM, Morris SL, King CH, Jacobs WR. 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 Oct 14; 100(21):12420-5. view on PubMed
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. Use of genetic profiling in leprosy to discriminate clinical forms of the disease. Science. 2003 Sep 12; 301(5639):1527-30. view on PubMed
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 Sep 30; 100(20):11207-10. view on PubMed
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. Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA. Biophys Chem. 2003 Sep; 105(2-3):361-70. view on PubMed
Strong M, Mallick P, Pellegrini M, Thompson MJ, 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. view on PubMed
Lee S, Eisenberg D. Seeded conversion of recombinant prion protein to a disulfide-bonded oligomer by a reduction-oxidation process. Nat Struct Biol. 2003 Sep; 10(9):725-30. view on PubMed
Diaz-Avalos R, Long C, Fontano E, Balbirnie M, Grothe R, Eisenberg D, Caspar DL. Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide. J Mol Biol. 2003 Jul 25; 330(5):1165-75. view on PubMed
Salwinski L, Eisenberg D. Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol. 2003 Jun; 13(3):377-82. view on PubMed
Freedland SJ, Pantuck AJ, Paik SH, Zisman A, Graeber TG, Eisenberg D, McBride WH, Nguyen D, Tso CL, Belldegrun AS. Heterogeneity of molecular targets on clonal cancer lines derived from a novel hormone-refractory prostate cancer tumor system. Prostate. 2003 Jun 01; 55(4):299-307. view on PubMed
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 May; 12(5):1097-108. view on PubMed
Cech TR, Eddy SR, Eisenberg D, Hersey K, Holtzman SH, Poste GH, Raikhel NV, Scheller RH, Singer DB, Waltham MC, National Academics Committee on Responsibilities of Authorship in the Biological Sciences. Sharing publication-related data and materials: responsibilities of authorship in the life sciences. Plant Physiol. 2003 May; 132(1):19-24. view on PubMed
Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D. The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs). Protein Sci. 2003 Apr; 12(4):832-47. view on PubMed
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 Apr 15; 100(8):4539-44. view on PubMed
Mura C, Katz JE, Clarke SG, 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 Mar 07; 326(5):1559-75. view on PubMed
McCarty AS, Kleiger G, Eisenberg D, Smale ST. Selective dimerization of a C2H2 zinc finger subfamily. Mol Cell. 2003 Feb; 11(2):459-70. view on PubMed
Anderson DH, Sawaya MR, Cascio D, Ernst W, Modlin R, Krensky A, Eisenberg D. Granulysin crystal structure and a structure-derived lytic mechanism. J Mol Biol. 2003 Jan 10; 325(2):355-65. view on PubMed
Eisenberg D. John T. Edsall as tutor and teacher. Biophys Chem. 2003; 100(1-3):91-3. view on PubMed
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 Dec 10; 99(25):16041-6. view on PubMed
Goulding CW, Parseghian A, Sawaya MR, Cascio D, Apostol MI, Gennaro ML, Eisenberg D. Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution. Protein Sci. 2002 Dec; 11(12):2887-93. view on PubMed
Gill HS, Pfluegl GM, Eisenberg D. Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation. Biochemistry. 2002 Aug 06; 41(31):9863-72. view on PubMed
Mallick P, Boutz DR, Eisenberg D, Yeates TO. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc Natl Acad Sci U S A. 2002 Jul 23; 99(15):9679-84. view on PubMed
Goulding CW, Sawaya MR, 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 Jun 04; 41(22):6920-7. view on PubMed
Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci. 2002 Jun; 11(6):1285-99. view on PubMed
Goulding CW, Apostol M, Anderson DH, Gill HS, Smith CV, Kuo MR, Yang JK, Waldo GS, Suh SW, Chauhan R, Kale A, Bachhawat N, Mande SC, Johnston JM, Lott JS, Baker EN, Arcus VL, Leys D, McLean KJ, Munro AW, Berendzen J, Sharma V, Park MS, Eisenberg D, Sacchettini J, Alber T, Rupp B, Jacobs W, Terwilliger TC. The TB structural genomics consortium: providing a structural foundation for drug discovery. Curr Drug Targets Infect Disord. 2002 Jun; 2(2):121-41. view on PubMed
Kleiger G, Grothe R, Mallick P, Eisenberg D. GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles. Biochemistry. 2002 May 14; 41(19):5990-7. view on PubMed
Deane CM, Salwinski L, Xenarios I, Eisenberg D. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics. 2002 May; 1(5):349-56. view on PubMed
Wang S, Mura C, Sawaya MR, Cascio D, Eisenberg D. Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets. Acta Crystallogr D Biol Crystallogr. 2002 Apr; 58(Pt 4):571-8. view on PubMed
Duan XJ, Xenarios I, Eisenberg D. Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database. Mol Cell Proteomics. 2002 Feb; 1(2):104-16. view on PubMed
Liu Y, Gotte G, Libonati M, Eisenberg D. Structures of the two 3D domain-swapped RNase A trimers. Protein Sci. 2002 Feb; 11(2):371-80. view on PubMed
Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002 Jan 01; 30(1):303-5. view on PubMed
Eisenberg DS, Kuriyan J, Richards FM. John T. Edsall and Advances in Protein Chemistry. Adv Protein Chem. 2002; 62:xi-xiv. view on PubMed
Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature. 2000 Jun 15; 405(6788):823-6. view on PubMed
Eisenberg D, Gill HS, Pfluegl GM, Rotstein SH. Structure-function relationships of glutamine synthetases. Biochim Biophys Acta. 2000 Mar 07; 1477(1-2):122-45. view on PubMed
Eisenberg D. How chaperones protect virgin proteins. Science. 1999 Aug 13; 285(5430):1021-2. view on PubMed
