Koide Laboratory - Publications

2024

  • Bang I, Hattori T, Leloup N, Corrado A, Nyamaa A, Koide A, Geles K, Buck E, Koide S. Selective targeting of oncogenic hotspot mutations of the HER2 extracellular domain. Nat Chem Biol. doi: 10.1038/s41589-024-01751-w.
  • Lebon C, Grossmann S, Mann G, Lindner F, Koide A, Koide S, Diepold A, Hantschel O. Cytosolic delivery of monobodies using the bacterial type III secretion system inhibits oncogenic BCR: ABL1 signaling.Cell Commun Signal. 22:500. doi: 10.1186/s12964-024-01874-6.
  • Whaby M, Ketavarapu G, Koide A, Mazzei M, Mintoo M, Glasser E, Patel U, Nasarre C, Sale MJ, McCormick F, Koide S, O'Bryan JP. Inhibition and degradation of NRAS with a pan-NRAS monobody. Oncogene. doi: 10.1038/s41388-024-03186-y.
  • Vanhauwaert R, Oury J, Vankerckhoven B, Steyaert C, Jensen SM, Vergoossen DLE, Kneip C, Santana L, Lim JL, Plomp JJ, Augustinus R, Koide S, Blanchetot C, Ulrichts P, Huijbers MG, Silence K, Burden SJ. ARGX-119 is an agonist antibody for human MuSK that reverses disease relapse in a mouse model of congenital myasthenic syndrome. Sci Transl Med. 16:eado7189. doi: 10.1126/scitranslmed.ado7189.
  • Li J, Li Y, Koide A, Kuang H, Torres VJ, Koide S, Wang DN, Traaseth NJ. Proton-coupled transport mechanism of the efflux pump NorA. Nat Commun. 15:4494. doi: 10.1038/s41467-024-48759-3.
  • Maso L, Rajak E, Bang I, Koide A, Hattori T, Neel BG, Koide S. Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes. Proc Natl Acad Sci U S A. 121:e2319029121. doi: 10.1073/pnas.2319029121.
  • Kiya M, Shiga S, Ding P, Koide S, Makabe K. β-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. J Mol Biol. 436:168405. doi: 10.1016/j.jmb.2023.168405.

2023

  • Ivanova EN, Shwetar J, Devlin JC, Buus TB, Gray-Gaillard S, Koide A, Cornelius A, Samanovic MI, Herrera A, Mimitou EP, Zhang C, Karmacharya T, Desvignes L, Ødum N, Smibert P, Ulrich RJ, Mulligan MJ, Koide S, Ruggles KV, Herati RS, Koralov SB. mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection. iScience. 26:108572. doi: 10.1016/j.isci.2023.108572.
  • Chapman JR, Paukner M, Leser M, Teng KW, Koide S, Holder M, Armache KJ, Becker C, Ueberheide B, Brenowitz M. Systematic Fe(II)-EDTA Method of Dose-Dependent Hydroxyl Radical Generation for Protein Oxidative Footprinting. Anal Chem. 95:18316. doi: 10.1021/acs.analchem.3c02319.
  • Ravn-Boess N, Roy N, Hattori T, Bready D, Donaldson H, Lawson C, Lapierre C, Korman A, Rodrick T, Liu E, Frenster JD, Stephan G, Wilcox J, Corrado AD, Cai J, Ronnen R, Wang S, Haddock S, Sabio Ortiz J, Mishkit O, Khodadadi-Jamayran A, Tsirigos A, Fenyö D, Zagzag D, Drube J, Hoffmann C, Perna F, Jones DR, Possemato R, Koide A, Koide S, Park CY, Placantonakis DG. The expression profile and tumorigenic mechanisms of CD97 (ADGRE5) in glioblastoma render it a targetable vulnerability. Cell Rep.42:113374. doi: 10.1016/j.celrep.2023.113374.
  • Meng Y, Garnish SE, Davies KA, Black KA, Leis AP, Horne CR, Hildebrand JM, Hoblos H, Fitzgibbon C, Young SN, Dite T, Dagley LF, Venkat A, Kannan N, Koide A, Koide S, Glukhova A, Czabotar PE, Murphy JM. Phosphorylation-dependent pseudokinase domain dimerization drives full-length MLKL oligomerization. Nat Commun. 2023 Oct 26;14:6804. doi: 10.1038/s41467-023-42255-w.
  • Akkapeddi P, Hattori T, Khan I, Glasser E, Koide A, Ketavarapu G, Whaby M, Zuberi M, Teng KW, Lefler J, Maso L, Bang I, Ostrowski MC, O'Bryan JP, Koide S. Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors. Proc Natl Acad Sci U S A. 120:e2302485120. doi: 10.1073/pnas.2302485120.
  • Koide A, Koide S. Use of Phage Display and Other Molecular Display Methods for the Development of Monobodies. Cold Spring Harb Protoc.doi: 10.1101/pdb.over107982. (PubMed)
  • Sha F, Kurosawa K, Glasser E, Ketavarapu G, Albazzaz S, Koide A, Koide S. Monobody inhibitor selective to the phosphatase domain of SHP2 and its use as a probe for quantifying SHP2 allosteric regulation. J Mol Biol. 168010. doi: 10.1016/j.jmb.2023.168010. (PubMed)

2022

  • Whaby M, Wallon L, Mazzei M, Khan I, Teng KW, Koide S, O'Bryan JP. Mutations in the α4-α5 allosteric lobe of RAS do not significantly impair RAS signaling or self-association. J Biol Chem. 2022 Nov 2:102661. doi: 10.1016/j.jbc.2022.102661. (PubMed)
  • Wallon L, Khan I, Teng KW, Koide A, Zuberi M, Li J, Ketavarapu G, Traaseth NJ, O'Bryan JP, Koide S. Inhibition of RAS-driven signaling and tumorigenesis with a pan-RAS monobody targeting the Switch I/II pocket. Proc Natl Acad Sci U S A. 119:e2204481119 (DOI)
  • Hattori T, Maso L, Araki KY, Koide A, Hayman J, Akkapeddi P, Bang I, Neel BG, Koide S. Creating MHC-restricted neoantigens with covalent inhibitors that can be targeted by immune therapy.Cancer Discovery (DOI)
  • Matsuzawa-Ishimoto Y, Yao X, Koide A, Ueberheide BM, Axelrad JE, Reis BS, Parsa R, Neil JA, Devlin JC, Rudensky E, Dewan MZ, Cammer M, Blumberg RS, Ding Y, Ruggles KV, Mucida D, Koide S, Cadwell K. The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death. Nature. Oct 5. (DOI)
  • Albert C, Bracaglia L, Koide A, DiRito J, Lysyy T, Harkins L, Edwards C, Richfield O, Grundler J, Zhou K, Denbaum E, Ketavarapu G, Hattori T, Perincheri S, Langford J, Feizi A, Haakinson D, Hosgood SA, Nicholson ML, Pober JS, Saltzman WM, Koide S*, Tietjen GT*. Monobody adapter for functional antibody display on nanoparticles for adaptable targeted delivery applications. Nat Commun 2022 Oct 11;13(1):5998. (DOI)
  • Rajsri KS, McRae MP, Simmons GW, Christodoulides NJ, Matz H, Dooley H, Koide A, Koide S, McDevitt JT. A Rapid and Sensitive Microfluidics-Based Tool for Seroprevalence Immunity Assessment of COVID-19 and Vaccination-Induced Humoral Antibody Response at the Point of Care. Biosensors. 12:621.(PubMed)
  • Teng KW, Koide A, Koide S. Engineering Binders with Exceptional Selectivity. Methods Mol Biol. 2491:143-154. (PubMed)
  • Brawley DN, Sauer DB, Li J, Zheng X, Koide A, Jedhe GS, Suwatthee T, Song J, Liu Z, Arora PS, Koide S, Torres VJ, Wang DN, Traaseth NJ. Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus.Nat Chem Biol. 2022 18:706-712. doi: 10.1038/s41589-022-00994-9. (PubMed)
  • Kermani AA, Burata OE, Koff BB, Koide A, Koide S, Stockbridge RB. Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates. Elife. 2022 Mar 7;11:e76766 (DOI)
  • Khan I, Koide A, Zuberi M, Ketavarapu G, Denbaum E, Teng KW, Rhett JM, Spencer-Smith R, Hobbs GA, Camp ER, Koide S, O'Bryan JP. Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants. Cell Rep. 38:110322. (DOI)

2021

  • Romero LA, Hattori T, A E Ali M, Ketavarapu G, Koide A, Park CY, Koide S. High-valency anti-CD99 antibodies toward the treatment of T cell acute lymphoblastic leukemia.J Mol Biol. 2021 Dec 24:167402 (DOI)
  • Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem doi.org/10.1039/D1MD00188D (RSC site)
  • Sulaiman et al. Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome. Nat Microbiol Aug 31. doi: 10.1038/s41564-021-00961-5. (PubMed)
  • Lopez-Redondo M, Fan S, Koide A, Koide S, Beckstein O, Stokes DL. Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. J Gen Physiol. 2021 Aug 2;153(8):e202112873. (PubMed)
  • Oury J, Zhang W, Leloup N, Koide A, Corrado AD, Ketavarapu G, Hattori T, Koide S, Burden SJ. Mechanism of disease and therapeutic rescue of Dok7 congenital myasthenia. Nature. 595:404 (Nature site)
  • Teng KW, Tsai ST, Hattori T, Fedele C, Koide A, Yang C, Hou X, Zhang Y, Neel BG, O'Bryan JP, Koide S. Selective and noncovalent targeting of RAS mutants for inhibition and degradation. Nat Commun. 12:2656. (PubMed)
  • Khan I, MarElia-Bennet C, Lefler J, Zuberi M, Denbaum E, Koide A, Connor DM, Broome AM, Pécot T, Timmers C, Ostrowski MC, Koide S, O'Bryan JP. Targeting the KRAS α4-α5 allosteric interface inhibits pancreatic cancer tumorigenesis. Small GTPases. May 5. Online ahead of print. (PubMed)
  • Garnish SE, Meng Y, Koide A, Sandow JJ, Denbaum E, Jacobsen AV, Yeung W, Samson AL, Horne CR, Fitzgibbon C, Young SN, Smith PPC, Webb AI, Petrie EJ, Hildebrand JM, Kannan N, Czabotar PE, Koide S, Murphy JM. Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis. Nat Commun. 12:2211 (PubMed)
  • Noval MG, Kaczmarek ME, Koide A, Rodriguez-Rodriguez BA, Louie P, Tada T, Hattori T, Panchenko T, Romero LA, Teng KW, Bazley A, de Vries M, Samanovic MI, Weiser JN, Aifantis I, Cangiarella J, Mulligan MJ, Desvignes L, Dittmann M, Landau NR, Aguero-Rosenfeld M, Koide S, Stapleford KA. Antibody isotype diversity against SARS-CoV-2 is associated with differential serum neutralization capacities.Sci Rep. 11:5538. (PubMed)
  • Hattori T, Koide A, Panchenko T, Romero LA, Teng KW, Corrado AD, Koide S.Multiplex bead binding assays using off-the-shelf components and common flow cytometers. J Immunol Methods. 490:112952. (PubMed)
  • Hattori T, Koide A, Noval MG, Panchenko T, Romero LA, Teng KW, Tada T, Landau NR, Stapleford KA, Koide .S The ACE2-binding Interface of SARS-CoV-2 Spike Inherently Deflects Immune Recognition. J Mol Biol. 2021 433:166748. (PubMed)

2020

  • Kermani AA, Macdonald CB, Burata OE, Ben Koff B, Koide A, Denbaum E, Koide S, Stockbridge RB. The structural basis of promiscuity in small multidrug resistance transporters. Nat Commun.Nov 27;11:6064. (PubMed)
  • Fedele C, Li S, Teng KW, Foster CJR, Peng D, Ran H, Mita P, Geer MJ, Hattori T, Koide A, Wang Y, Tang KH, Leinwand J, Wang W, Diskin B, Deng J, Chen T, Dolgalev I, Ozerdem U, Miller G, Koide S, Wong KK, Neel BG. SHP2 inhibition diminishes KRASG12C cycling and promotes tumor microenvironment remodeling. J Exp Med.218:e20201414.(PubMed)
  • Salzman GS, Zhang S, Fernandez CG, Araç D, Koide S. Specific and direct modulation of the interaction between adhesion GPCR GPR56/ADGRG1 and tissue transglutaminase 2 using synthetic ligands. Sci Rep. Oct 9;10:16912. (PubMed)
  • Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. Elife. Sep 1:e61350.(PubMed)
  • La Sala G, Michiels C, Kükenshöner T, Brandstoetter T, Maurer B, Koide A, Lau K, Pojer F, Koide S, Sexl V, Dumoutier L, Hantschel O. Selective inhibition of STAT3 signaling using monobodies targeting the coiled-coil and N-terminal domains. Nat Commun. 2020 Aug 17;11(1):4115. (PubMed)
  • Petrie EJ, Birkinshaw RW, Koide A, Denbaum E, Hildebrand JM, Garnish SE, Davies KA, Sandow JJ, Samson AL, Gavin X, Fitzgibbon C, Young SN, Hennessy PJ, Smith PPC, Webb AI, Czabotar PE, Koide S, Murphy JM. Identification of MLKL membrane translocation as a checkpoint in necroptotic cell death using Monobodies. Proc Natl Acad Sci U S A. 117(15):8468-8475. (PubMed)
  • Lee KY, Fang Z, Enomoto M, Gasmi-Seabrook G, Zheng L, Koide S, Ikura M, Marshall CB. Two Distinct Structures of Membrane-Associated Homodimers of GTP- and GDP-Bound KRAS4B Revealed by Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl. 59(27):11037-11045. (PubMed)
  • Hantschel O, Biancalana M, Koide S. Monobodies as enabling tools for structural and mechanistic biology. Curr Opin Struct Biol. 60:167-174. (PubMed)

2019

  • Röck R, Mayrhofer JE, Torres-Quesada O, Enzler F, Raffeiner A, Raffeiner P, Feichtner A, Huber RG, Koide S, Taylor SS, Troppmair J, Stefan E. BRAF inhibitors promote intermediate BRAF(V600E) conformations and binary interactions with activated RAS. Sci Adv. 5:eaav8463. (PubMed)
  • Koide S. Repurposing off-the-shelf antihelix antibodies for enabling structural biology. Proc Natl Acad Sci U S A. 116:17611-17613. (PubMed)
  • Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D. Allosteric modulation of a human protein kinase with monobodies. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13937-13942. (PubMed)
  • Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. ACS Cent Sci. 5:852-866. (PubMed)

2018

  • Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat Chem Biol. 2018 Jul 16. doi: 10.1038/s41589-018-0099-z. [Epub ahead of print] (PubMed)
  • Last NB, Stockbridge RB, Wilson AE, Shane T, Kolmakova-Partensky L, Koide A, Koide S, Miller C. A CLC-type F(-)/H(+) antiporter in ion-swapped conformations. Nat Struct Mol Biol. 25:601-606. (PubMed)
  • Tanaka SI, Takahashi T, Koide A, Iwamoto R, Koikeda S, Koide S. Monobody-mediated alteration of lipase substrate specificity. ACS Chem Biol. 2018 May 14. doi: 10.1021/acschembio.8b00384. (PubMed)
  • Hattori T, Koide S. Next-generation antibodies for post-translational modifications. Curr Opin Struct Biol. 51:141-148. (PubMed)
  • Makabe K, Nakamura T, Dhar D, Ikura T, Koide S, Kuwajima K. An Overlapping Region between the Two Terminal Folding Units of the Outer Surface Protein A (OspA) Controls Its Folding Behavior. J Mol Biol. 2018 Apr 27. doi: 10.1016/j.jmb.2018.04.025 (PubMed)
  • Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, Koide S, Kossiakoff AA, Li S, Carragher B, Potter CS, Tang WJ. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. Elife. e33572. doi: 10.7554/eLife.33572. (PubMed)
  • Diver MM, Pedi L, Koide A, Koide S, Long SB. Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature.553:526-529. (PubMed)

2017

  • Reckel S, Gehin C, Tardivon D, Georgeon S, Kükenshöner T, Löhr F, Koide A, Buchner L, Panjkovich A, Reynaud A, Pinho S, Gerig B, Svergun D, Pojer F, Güntert P, Dötsch V, Koide S, Gavin AC, Hantschel O. Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. Nat Commun. 8:2101 (PubMed)
  • Ghosh E, Srivastava A, Baidya M, Kumari P, Dwivedi H, Nidhi K, Ranjan R, Dogra S, Koide A, Yadav PN, Sidhu SS, Koide S, Shukla AK. A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis. Nat Nanotechnol. 12:1190-1198. (PubMed)
  • Salzman GS, Zhang S, Gupta A, Koide A, Koide S*, Araç D*. Stachel-independent modulation of GPR56/ADGRG1 signaling by synthetic ligands directed to its extracellular region. Proc Natl Acad Sci U S A 14:10095-100.(PubMed)
  • Spencer-Smith R, Li L, Prasad S, Koide A, Koide S, O'Bryan JP. Targeting the α4-α5 interface of RAS results in multiple levels of inhibition. Small GTPases. 2017 Jul 10:0. doi: 10.1080/21541248.2017.1333188. [Epub ahead of print] (PubMed)
  • Rizk SS, Mukherjee S, Koide A, Koide S, Kossiakoff AA. Targeted rescue of cancer-associated IDH1 mutant activity using an engineered synthetic antibody. Sci Rep.7:556. (PubMed)
  • Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O. Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. J Mol Biol. 429:1364-1380. Epub 2017 Mar 25. (PubMed)
  • Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci. 26:910-924. Epub 2017 Mar 24. (PubMed)
  • Bowman A, Koide A, Goodman JS, Colling ME, Zinne D, Koide S, Ladurner AG. sNASP and ASF1A function through both competitive and compatible modes of histone binding. Nucleic Acids Res. 45:643-656. Epub 2016 Oct 5. (PubMed)
  • Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Rajakulendran T, Dowdell E, Okur MN, Dementieva I, Sicheri F, Therrien M, Hancock JF, Ikura M, Koide S*, O’Bryan JP*. Inhibition of RAS function through targeting an allosteric regulatory site. Nature Chem Biol 13:62-68. Epub 2016 Nov 7.(PubMed)
  • Sachleben JR, Adhikari AN, Gawlak G, Hoey RJ, Liu G, Joachimiak A, Montelione GT, Sosnick TR, Koide S. Aromatic Claw: A new fold with high aromatic content that evades structural prediction. Protein Sci. Protein Sc 26:208-217. Epub 2016 Nov 10 (PubMed)

2016

  • Salzman GS, Ackerman SD, Ding C, Koide A, Leon K, Luo R, Stoveken HM, Fernandez CG, Tall GG, Piao X, Monk KR, Koide S*, Araç D*. Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains. Neuron.91:1292-304. (PubMed)
  • Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol. 2016 428:4100-4114. (PubMed)
  • Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S. Allosteric Inhibition of Bcr-Abl Kinase by High-Affinity Monobody Inhibitors Directed to the SH2-Kinase Interface. J Biol Chem. 291:8836-47. (PubMed)
  • Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc Natl Acad Sci U S A. 113:2092-7. (PubMed)

2015

  • Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. eLife 4:e10150. (PubMed)
  • Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One. 10:e0139695. (PubMed)
  • Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, Newstead S. Crystal structures of a double-barrelled fluoride ion channel. Nature. 525:548-51 (PubMed)
  • Tanaka SI, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S. Monobody-mediated alteration of enzyme specificity. Nat Chem Biol. 11:762-4 (PubMed)
  • Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A. Architecture of the fungal nuclear pore inner ring complex. Science. 350:56-64 (PubMed)
  • Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics. 14:2833-47 (PubMed).
  • Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods. 12:725-31. (PubMed)
  • Miersch S, Li Z, Hanna R, McLaughlin ME, Hornsby M, Matsuguchi T, Paduch M, Sääf A, Wells J, Koide S, Kossiakoff A, Sidhu SS. Scalable high throughput selection from phage-displayed synthetic antibody libraries. J Vis Exp. (95):51492. (PubMed)
  • Biancalana M, Makabe K, Yan S, Koide S. Aromatic cluster mutations produce focal modulations of β-sheet structure. Protein Sci. 24:841-9. (PubMed)

2014

  • Zhang X, Hoey R, Koide A, Dolios G, Paduch M, Nguyen P, Wu X, Li Y, Wagner SL, Wang R, Koide S, Sisodia SS.Synthetic Antibody Fragment Targeting Nicastrin Affects Assembly and Trafficking of γ-Secretase.J Biol Chem. 289:34851-61. (PubMed)
  • Stockbridge RB, Koide A, Miller C, Koide S. Proof of dual-topology architecture of Fluc F- channels with monobody blockers. Nat Commun. 5:5120. (PubMed)
  • Jose CC, Xu B, Jagannathan L, Trac C, Mallela RK, Hattori T, Lai D, Koide S, Schones DE, Cuddapah S.Epigenetic dysregulation by nickel through repressive chromatin domain disruption.Proc Natl Acad Sci U S A.111:14631-6.(PubMed)
  • Koide S, Kortemme T. Editorial overview: Engineering and design: raising the bar through innovation and integration.Curr Opin Struct Biol. 27:vi-viii. (PubMed)
  • Shukla AK, Westfield GH, Xiao K, Reis RI, Huang LY, Tripathi-Shukla P, et al. Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature published online 22 June 2014. (PubMed)
  • Yasui N, Findlay GM, Gish GD, Hsiung MS, Huang J, Tucholska M, Taylor L, Smith L, Boldridge WC, Koide A, Pawson T, Koide S. Directed Network Wiring Identifies a Key Protein Interaction in Embryonic Stem Cell Differentiation. Mol Cell. 54:1034-41. (PubMed)

2013

  • Sha F, Gencer EB, Georgeon S, Koide A, Yasui N, Koide S, Hantschel O. (2013) Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proc Natl Acad Sci U S A. 110:14924-9. (PubMed) [Highlighted by Faculty of 1000.]
  • Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. (2013) Recombinant antibodies to histone post-translational modifications. Nat Methods 10:992-5. (PubMed)
  • McCord LA, Liang WG, Dowdell E, Kalas V, Hoey RJ, Koide A, Koide S, Tang WJ. (2013) Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme. Proc Natl Acad Sci U S A. 110:13827-32. (PubMed)
  • Shukla AK, Manglik A, Kruse AC, Xiao K, Reis RI, Tseng WC, Staus DP, Hilger D, Uysal S, Huang LY, Paduch M, Tripathi-Shukla P, Koide A, Koide S, Weis WI, Kossiakoff AA, Kobilka BK, Lefkowitz RJ. (2013) Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature. 497:137-41. (PubMed) [Highlighted by Faculty of 1000.]
  • Koide S, Huang J. (2013) Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping. Methods Enzymol. 523:285-302. (PubMed)
  • Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nei R, Koide S. (2013) Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. Proc Natl Acad Sci U S A. 110:2099-2104. (PubMed) [Highlighted by Faculty of 1000.]
  • Persson H, Ye W, Wernimont A, Adams JJ, Koide A, Koide S, Lam R, Sidhu SS. CDR-H3 Diversity Is Not Required for Antigen Recognition by Synthetic Antibodies. J Mol Biol. 425:803-11. (PubMed)
2012
  • Paduch M, Koide A, Uysal S, Rizk SS, Koide S, Kossiakoff AA. (2013) Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods. 2012 Dec 29. [Epub ahead of print] (PubMed)
  • Gibreth RN, Koide S. (2012) Structural Insights for Engineering Binding Proteins Based on Non-Antibody Scaffolds. Curr Opin Struct Biol, 22:413-20. (PubMed)
  • Koide S, Koide A, Lipovsek D. (2012) Target-Binding Proteins Based on the 10th Human Fibronectin Type III Domain ((10)Fn3). Methods Enzymol. 503, 135-56. (PubMed)
  • Nishikori S, Hattori T, Fuchs SM, Yasui N, Wojcik J, Koide A, Strahl BD Koide S. (2012) Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. J Mol Biol. 424:391-9. (PubMed)
  • Kitahara R, Simorellis AK, Hata K, Maeno A, Yokoyama S, Koide S, Akasaka K. (2012) A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A. Biophys J. 102:916-26. (PubMed)
  • Miller KR, Koide A, Leung B, Fitzsimmons J, Yoder B, Yuan H, Jay M, Sidhu SS, Koide S*, Collins EJ*. (2012) T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. PloS One. 7:e43746. (PubMed)
  • Zhang X, Hoey RJ, Lin G, Koide A, Leung B, Ahn K, Dolios G, Paduch M, Ikeuchi T, Wang R, Li Y, Koide S*, Sisodia SS*. (2012) Identification of a TPR-like domain in the Nicastrin subunit of gamma-secretase using synthetic antibodies. Proc Natl Acad Sci U S A.109:8534-8539. (PubMed)
  • Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S. (2012) Teaching an Old Scaffold New Tricks: Monobodies Constructed Using Alternative Surfaces of the FN3 Scaffold. J Mol Biol. 415:393-405. (PubMed)
2011
  • Uysal S, Cuello LG, Cortes DM, Koide S, Kossiakoff AA, Perozo E. (2011) Mechanism of activation gating in the full-length KcsA K+ channel. Proc Natl Acad Sci U S A. 108:11896-9. (PubMed)
  • Grebien F, Hantschel O, Wojcik J, Kaupe I, Kovacic B, Wyrzucki AM, Gish GD, Cerny-Reiterer S, Koide A, Beug H, Pawson T, Valent P, Koide S, Superti-Furga G. (2011) Targeting the SH2-Kinase Interface in Bcr-Abl Inhibits Leukemogenesis. Cell. 147:306-19. (PubMed)
  • Gilbreth RG, Truong K, Madu I, Koide A, Wojcik J, Li NS, Piccirilli JA, Chen Y & Koide S. (2011) Isoform-specific monobody inhibitors of small ubiquitin-like modifiers engineered using structure-guided library design. Proc Natl Acad Sci U S A 108, 7751-7756. (PubMed)
  • Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel D P, Koide S, Kossiakoff AA & Piccirilli, J. A. (2011) A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol. 18, 100-106. (PubMed)
  • Colwill K, Renewable Protein Binder Working Group, Graslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods. 2011;8:551-8. (PubMed)
2010
  • Biancalana M & Koide S. (2010) Molecular mechanism of thioflavin-T binding to peptide self-assemblies. BBA Proteins and Proteomics, 1804, 1405-1412. (PubMed)
  • Shemon AN, Heil GL, Granovsky AE, Clark MM, McElheny D, Chimon A, Rosner MR, Koide S. (2010) Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands. PloS One. 5:e10479. (PubMed)
  • Huang J & Koide S. (2010) Rational conversion of affinity clamps into label-free sensors for peptide motifs by designed allostery. ACS Chemical Biology 5, 273-277. (PubMed)
  • Wojcik J, Hantschel O, Grebien F, Kaupe I, Bennett KL, Barkinge J, Jones RB, Koide A, Superti-Furga G & Koide S. (2010) A potent and highly specific inhibitor of c-Abl1 SH2 domain. Nature Struct Mol Biol 17, 519–527. (PubMed)
  • Biancalana M, Makabe K, & Koide S. (2010) Minimalist design of water-soluble cross-β architecture. Proc Natl Acad Sci U S A, 107, 3469–3474. (PubMed)
2009
  • Koide S. (2009) Generation of novel protein functions by domain combinations and rearrangements. Curr Opin Biotechnol, 20, 398-404. (PubMed)
  • Koide S. (2009) Engineering synthetic chaperones for crystallization. Curr Opin Struct Biol, 19, 449-457. (PubMed)
  • Koide S & Sidhu SS. (2009) The importance of being tyrosine: Lessons in molecular recognition from minimalist synthetic binding proteins. ACS Chemical Biology, 4, 325-334. [The second most accessed article of the journal, April-June 2009] (PubMed)
  • Takacs Z, et al. (2009) Designer toxins built on animal neurotoxin scaffolds: target-based library and high-throughput selection of a specific Kv1.3 channel inhibitor. Proc Natl Acad Sci U S A, 106, 22211–6. (PubMed)
  • Huang J, Nagy S, Koide A, Rock RS & Koide S. (2009) A peptide tag system for facile purification and single-molecule immobilization. Biochemistry, 48, 11834–11836. (PubMed)
  • Wu C, Biancalana M, Koide S & Shea J-E. (2009) Interaction modes of thioflavin T with the surface of peptide self-assembly mimics. J Mol Biol, 394, 627-633. (PubMed)
  • Koide A, Wojcik J, Gilbreth RN, Reichel A, Piehler J & Koide S. (2009) Accelerating phage-display library selection by reversible and site-specific biotinylation. Protein Engineering, Design and Selection, 22, 685-690. (PubMed)
  • Huang J, Makabe K, Biancalana M, Koide A & Koide S. (2009) Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. J Mol Biol, 392, 1221-1231. (PubMed)
  • Shemon A, Eves E, Clark MC, Heil G, Granovsky A, Zeng L, Imamoto A, Koide S & Rosner MR. (2009) Raf kinase inhibitory protein protects cells against locostatin-mediated inhibition of migration. PLoS One, 4, e6028. (PubMed)
  • Granovsky AE, Clark MC, McElheny D, Heil G, Hong J, Liu X, Kim Y, Joachimiak G, Joachimiak A, Koide S* & Rosner MR*. (2009) Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism. Mol Cell Biol, 29, 1306-1320. (PubMed)
  • Uysal S, Vásquez V, Tereshko V, Esaki K, Fellouse FA, Sidhu SS, Koide S, Perozo E & Kossiakoff AA. (2009) The crystal structure of full-Length KcsA in its closed conformation. Proc Natl Acad Sci U S A, 106, 6644-6649. (PubMed)
  • Biancalana M, Makabe K, Koide A & Koide S. (2009) Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies. J Mol Biol, 385, 1052-1063. (PubMed)
2008
  • Makabe K & Koide S. (2008) The promiscuity of beta-strand pairing allows for rational design of beta-sheet flips. J Am Chem Soc, 130, 14370-14371. (PubMed)
  • Biancalana M, Makabe K, Koide A & Koide S. (2008) Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics. J Mol Biol, 383, 205-213. (PubMed)
  • Dutta S, Koide A & Koide S. (2008) High-throughput analysis of the protein sequence-stability landscape using a quantitative "yeast surface two-hybrid" system and fragment reconstitution. J Mol Biol, 382, 721-733. (PubMed)
  • Gilbreth RN, Esaki K, Koide A, Sidhu SS & Koide S. (2008). A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. J Mol Biol, 381, 407-418. (PubMed)
  • Kossiakoff AA & Koide S. (2008) Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. Curr Opin Struct Biol. 18, 499-506. (PubMed)
  • Tereshko V, Uysal S, Koide A, Margalef K, Koide S*, Kossiakoff AA* (*co-corresponding authors). (2008) Toward chaperone-assisted crystallography: Protein engineering enhancement of crystal packing and x-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Sci, 17,1175-87. (PubMed)
  • Huang J, Koide A, Makabe K & Koide S. (2008) Design of protein function leaps by directed domain interface evolution. Proc Natl Acad Sci U S A, 105, 6578-6583. (PubMed)
  • Makabe K, Biancalana K, Yan S, Tereshko V, Gawlak G, Miller-Auer H, Meredith SC & Koide S. (2008) High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble β-sheet scaffold. J Mol Biol 378, 459-467. (PubMed)
  • Ye J, Tereshko V, Frederiksen JK, Fellouse FA, Koide A, Sidhu SS, Koide S*, Kossiakoff AA* & Piccirilli JA*. (2008) Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc Natl Acad Sci U S A, 105, 82-87. (PubMed)
  • Mallik B, Zhang L, Koide S & Morikis D. (2008) On the pH-dependent stability change of the tenth human fibronectin type III domain: a computational Study. Biotechnol Prog 24, 48-55. (PubMed)
2007
  • Makabe K, Yan S, Tereshko V, Gawlak G, & Koide S. (2007) β-Strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of β-strand pairing. J Am Chem Soc, 129, 14661-14669. (PubMed)
  • Koide A, Tereshko V, Uysal S, Margalef K, Kossiakoff AA & Koide S. (2007) Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. J Mol Biol, 373, 941-953. (PubMed)
  • Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ, Koide A, Jhurani P, Vasser M, Wiesmann C, Kossiakoff AA, Koide S* & Sidhu SS*. (*co-corresponding authors) (2007) High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol, 373, 924-940. (PubMed)
  • Koide A., Gilbreth R, Esaki K, Tereshko V., Koide S. (2007) High-affinity single-domain binding proteins with a binary code interface. Proc Natl Acad Sci U S A, 104,6632-6637. (PubMed)
  • Yan S, Gawlak G, Makabe K, Tereshko V, Koide A & Koide S. (2007) Hydrophobic Surface Burial is the Major Stability Determinant of a Flat, Single-Layer β-Sheet. J Mol Biol, 368,230-243. (PubMed)
  • Koide A, Zhao C, Naganuma M, Abrams J, Deighton-Collins S, Skafar DF & Koide S. (2007) Identification of regions within the F domain of the human estrogen receptor-alpha that are important for modulating transactivation and protein-protein interactions. Mol Endocrinol, 21, 829-847. (PubMed)
  • Koide A & Koide S. (2007). Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods Mol Biol 352, 95-109. (PubMed)
  • Sidhu SS & Koide S. (2007). Phage display for engineering and analyzing molecular recognition interfaces. Curr Opin Struct Biol, 17, 481-487. (PubMed)
  • Koide S. (2007). Minimalist engineering of protein-protein interactions. Chemistry and Biology (Tokyo), 45, 785-791.
2006
  • Clark MC, McElheny D, Wojcik J, Kurutz J, Rosner MR & Koide S. (2006) NMR assignment of rat Raf kinase inhibitor protein. J Biomol NMR, 36S, 5. (PubMed)
  • Huang J, Koide A, Nettle, KW, Greene GL & Koide S. (2006) Conformation-specific affinity purification of proteins using engineered binding proteins: Application to the estrogen receptor. Protein Expr Purif, 47, 384-354. (PubMed)
  • Makabe K, Tereshko V, Gawlak G, Yan S, Koide S. (2006) Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering. Protein Sci, 15, 1907-1914. (PubMed)
  • Makabe K, McElheny D, Tereshko V, Hilyard A, Gawlak G, Yan S, Koide A & Koide S. (2006). Atomic structures of peptide self-assembly mimics. Proc Natl Acad Sci U S A 103, 17753-17758. (PubMed)
2005
  • Koide S, Yang X, Huang X, Dunn JJ & Luft BJ. (2005) Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA. J Mol Biol. 350, 290-299. (PubMed)
  • Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR & Freed KF. (2005) Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry 44, 9691-9702. (PubMed)
  • Dutta S, Batori V, Koide A & Koide S. (2005) High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein Sci. 14, 2838-2848. (PubMed)
  • Skafar DF & Koide S. (2006) Understanding the human estrogen receptor-alpha using targeted mutagenesis. Mol Cell Endocrinol 246, 83-90. (PubMed)
2004
  • Murphy WL, Mercurius KO, Koide S & Mrksich M. (2004) Substrates for Cell Adhesion Prepared via Active Site-Directed Immobilization of a Protein Domain. Langmuir 20 1026-1030. (PubMed)
  • Yan, S., Gawlak, G., Smith, J., Silver, L., Koide, A., & Koide, S. (2004) Conformational Heterogeneity of an Equilibrium Folding Intermediate Quantified and Mapped by Scanning Mutagenesis. J. Mol. Biol. 338, 811-825. (PubMed)
  • Karatan, E., Merguerian, M., Han, Z., Scholle, M.D., Koide, S. & Kay, B.K. (2004) Molecular Recognition Properties of FN3 Monobodies that Bind the Src SH3 Domain. Chem. Biol. 11, 835-844. (PubMed)
2003
  • Richards J, Miller M, Abend J, Koide A, Koide S, & Dewhurst S. (2003) Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin. J Mol Biol. 326,1475-88. (PubMed)
  • Zhao C, Koide A, Abrams J, Deighton-Collins S, Martinez A, Schwartz JA, Koide S. & Skafar DF. (2003). Mutation of Leu-536 in human estrogen receptor-alpha alters the coupling between ligand binding, transcription activation, and receptor conformation. J Biol Chem 278, 27278-86. (PubMed)
  • Hertadi R, Gruswitz F, Silver L, Koide A, Koide S, Arakawa H. & Ikai A. (2003). Unfolding Mechanics of Multiple OspA Substructures Investigated with Single Molecule Force Spectroscopy. J Mol Biol. 333, 993-1002. (PubMed)
2002
  • Batori V, Koide A & Koide S. (2002) Exploring the potential of the monobody scaffold: Effects of loop elongation on the stability of a fibronectin type III domain. Protein Engineering, 15, 1015-1020. (PubMed)
  • Koide A, Abbatiello S, Rothgery L. & Koide S. (2002) Probing protein conformational changes in living cells using designer binding proteins: application to the estrogen receptor. Proc Natl Acad Sci USA, 99, 1253-1258. (PubMed)
  • Yan S, Kennedy SD. & Koide S. (2002) Thermodynamic and kinetic exploration of the energy landscape of Borrelia OspA by native state hydrogen exchange. J Mol Biol 323, 363-375. (PubMed)
  • Pawley NH., Koide S. and Nicholson L. (2002) Backbone Dynamics and Thermodynamics of Outer Surface Protein A. J Mol Biol 324, 991-1002. (PubMed)
  • Nakagawa T, Shimizu H, Link K, Koide A, Koide S & Tamura A. (2002) Calorimetric dissection of thermal unfolding of OspA, a predominantly b-sheet protein containing a single-layer β-sheet. J. Mol. Biol. 323, 751-762. (PubMed)
2001
  • Kumaran D, Eswaramoorthy S, Luft BJ, Koide S, Dunn JJ, Lawson CL & Swaminathan S. (2001) Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete Borrelia burgdorferi. EMBO J. 20, 971-978. (PubMed)
  • Yudt MR & Koide S. (2001) Preventing estrogen receptor action with dimer-interface peptides. Steroids 66, 549-558. (PubMed)
  • Huang X, Nakagawa T, Tamura A, Link K, Koide A & Koide S. (2001) Formation of the single-layer β-sheet of Borrelia burgdorferi OspA in the absence of the C-terminal capping globular domain. J. Mol. Biol. 308, 367-375. (PubMed)
  • Koide A, Jordan M, Horner S, Batori V & Koide S. (2001) Stabilization of a fibronectin type III domain by removal of unfavorable electrostatic interactions on the surface. Biochemistry 40, 10326-10333. (PubMed)
  • Ohnishi S, Koide A & Koide S. (2001) The importance of turn formation in the fibril formation of a polar β-hairpin peptide derived from the OspA single-layer β-sheet. Protein Science, 10, 2083-2092. (PubMed)
  • Pawley N, Wang C, Koide S & Nicholson L. (2001) An improved method for distinguishing between anisotropic tumbling and chemical exchange in analysis of 15N relaxation parameter. J. Biomol. NMR 20, 149-165. (PubMed)
2000
  • Koide S, Huang X, Link K, Koide A, Bu Z. & Engelman DM. (2000) Design of single-layer β-sheets without a hydrophobic core. Nature 403, 456-460. (PubMed)
  • Ohnishi S, Koide A. & Koide S. (2000) Solution conformation and amyloid-like fibril formation of a polar β-hairpin peptide derived from the OspA single-layer β-sheet. J Mol Biol 301, 477-489. (PubMed)
  • Ding W, Huang X, Yang X, Dunn JJ, Luft BJ, Koide S. & Lawson CL. (2000) Identification of a key protective B-cell epitope in Lyme disease antigen OspA. J Mol Biol. 302, 1153-1164. (PubMed)
  • Ohnishi S & Koide S. (2000) Proteins without a hydrophobic core: structure and stability. Proteins, Nucleic Acids and Enzymes (Tokyo), 45, 2502-2510. (PubMed)
1999 and earlier
  • Koide, S., Bu, Z.,Risal, D., Pham, T.-N. & Engelman, D. M. (1999) Multi-step denaturation of Borrelia burgdorferi OspA, a protein containing a single-layer β-sheet. Biochemistry 38, 4757-4767. (PubMed)
  • Huang X., Dunn JJ, Lawson CL, Luft BJ & Koide S. (1999) 1H, 13C, and 15N NMR backbone assignments of 37 kDa surface antigen OspC from Borrelia burgdorferi. J Biomol NMR 14, 283-284. (PubMed)
  • Pham, T.-N., Koide, A. & Koide, S. (1998) A stable single-layer β-sheet without a hydrophobic core. Nature Struct. Biol. 5, 115-119. (PubMed)
  • Pham, T. N. & Koide, S. (1998) NMR studies of Borrelia burgdorferi OspA, a 28 kDa protein containing a single-layer β-sheet. J. Biomol. NMR 11, 407-414. (PubMed)
  • Huang, X., Yang, X., Luft, B. J. & Koide, S. (1998) NMR identification of epitopes of Lyme disease antigen OspA. J. Mol. Biol., 281, 61-67. (PubMed)
  • Koide, A., Bailey, C. W., Huang, X. & Koide, S. (1998) Fibronecting type III domain as a scaffold for novel ligand binding proteins. J. Mol. Biol. 284, 1141-1151. (PubMed)
  • Bu, Z., Koide, S. & Engelman, D. M. (1998) A solution SAXS study of Borrelia burgdorferi OspA, a protein containing a single-layer β-sheet. Protein Science 7, 2681-2683. (PubMed)