Koide Laboratory
Publications
Publications are assigned permanent serial numbers. Add each new paper as an individual file in src/data/publications/ using the next serial number.
2026
186.
Kainth AS, Sirjoosingh P, Werner MS, Gupta A, Koide A, Koide S, Ruthenburg AJ. Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state. Mol Cell. doi: 10.1016/j.molcel.2026.08.008.DOI
185.
Hu Z, Patel UR, Glasser E, Koide A, Koide S. Protein Engineering-Enabled Cryo-EM Investigation of Small GTPases.J Mol Biol. 438:169860. doi: 10.1016/j.jmb.2026.169860 .DOI
184.
Suh SM, Ben-Zvi B, Talbott JM, Manoj N, Nelson BM, Hughes RR, Haug GC, Koide S, Paton RS, Raj M, Diao T. TagC-RED: An Infrared-Triggered Retro-Ene Reaction for Deep-Tissue Bioconjugation.J Am Chem Soc. 148:19738-19749. doi: 10.1021/jacs.6c01581 .DOI
183.
Pillai R, Rashidfarrokhi A, Hao Y, Wu WL, Mancini MCS, Karadal-Ferrena B, Dimitriadoy SG, Cross M, Yeaton AH, Huang SM, Bhutkar A, Herrera AM, Rajalingam S, Hayashi M, Huang KL, Bartnicki E, Zavitsanou AM, Ivanova E, Wohlhieter C, LeBoeuf SE, Chen T, Loomis CA, Kulicke R, Davis FP, Stransky N, Smolen GA, Tsay JJ, Simabuco FM, Rudin CM, Moreira AL, Khanna KM, Pass HI, Wong KK, Koide S, Tsirigos A, Koralov SB, Papagiannakopoulos T.LIF-Induced Tumor Plasticity Establishes an Immunosuppressive Myeloid Niche in LKB1-Mutant Lung Cancer. Cancer Discov.16:1436-1455. doi: 10.1158/2159-8290.CD-25-0470 .DOI
182.
Bossowski JP, Pillai R, Kilian J, Wong Lau A, Nakamura M, Rashidfarrokhi A, Hao Y, Li R, Wu K, Hattori T, Glasser E, Koide A, Wang L, Moreira AL, Hajdu C, Rajalingam S, LeBoeuf SE, Le H, Lee S, Oh JW, Joe C, Kim H, Ock CY, Lee SH, Wang H, Patel AAH, Sayin VI, Tsirigos A, Wong KK, Koralov SB, Pende M, Sánchez-Rivera FJ, Simeone DM, Zervantonakis IK, Koide S, Papagiannakopoulos T. The integrated stress response promotes immune evasion through lipocalin 2.Nature. 652:1329-1338. doi: 10.1038/s41586-026-10143-0 .DOI
2025
181.
Maso L, Mosure SA, Rodriguez-Aponte SA, Pizzo A, Mensah DN, Southard M, Sze S, Ahmed T, Vash B, Hattori T, Rajak E, Koide A, Neel BG, Koide S, Liu W, Toenjes ST, Jardine PDS, Chopra R, Rader C, Stopfer LE. Engineered antibodies that stabilize drug-modified KRASG12C neoantigens enable selective and potent cross-HLA immunotherapy.Nat Commun. 2025 16:11264. doi: 10.1038/s41467-025-66132-w .DOI
180.
Hattori T, Wang M, Corrado AD, Gross S, Fang M, Bang I, Roy N, Berezniuk I, Donaldson H, Groff K, Ravn-Boess N, Koide A, Placantonakis DG, Park CY, Koide S. Engineering antibody-drug conjugates targeting an adhesion GPCR, CD97. Proc Natl Acad Sci U S A. 122:e2516627122. DOI: 10.1073/pnas.2516627122 .DOI
179.
Maso L, Rajak E, Hattori T, Hu Z, Koide A, Neel BG, Koide S. Generation of actionable, cancer-specific neoantigens from KRAS(G12C) with adagrasib. Proc Natl Acad Sci U S A.122:e2509012122. doi: 10.1073/pnas.2509012122 .DOI
178.
Du J, Chen H, You J, Hu W, Liu J, Lu Q, Zhang Y, Gao J, Lin MJ, Foster CJR, Rao E, Cammer M, Yin W, Koide S, Lu CP, Chen W, Lou J, Wang J. Proximity between LAG-3 and the T cell receptor guides suppression of T cell activation and autoimmunity.Cell. 188:4025-4042.e20. doi: 10.1016/j.cell.2025.06.004 .DOI
2024
177.
Riso M, Shah RN, Koide A, Ruthenburg AJ, Koide S, Hattori T. Binding mode–guided development of high-performance antibodies targeting site-specific posttranslational modifications. Proc Natl Acad Sci U S A.122:e2411720121. doi: 10.1073/pnas.2411720121 .DOI
176.
Schmidt N, Kumar A, Korf L, Dinh-Fricke AV, Abendroth F, Koide A, Linne U, Rakwalska-Bange M, Koide S, Essen LO, Vázquez O, Hantschel O. Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase.Nat Commun. 2024 Dec 23;15(1):10724. doi: 10.1038/s41467-024-54901-y .DOI
175.
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 .DOI
174.
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 .DOI
173.
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 .DOI
172.
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 .DOI
171.
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 .DOI
170.
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 .DOI
169.
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 .DOI
2023
168.
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 .DOI
167.
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 .DOI
166.
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 .DOI
165.
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 .DOI
164.
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 .DOI
163.
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 )PubMed
2022
161.
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 )PubMed
160.
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 )DOI
159.
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 )DOI
158.
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 )DOI
157.
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 )DOI
156.
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 )PubMed
155.
Teng KW, Koide A, Koide S. Engineering Binders with Exceptional Selectivity. Methods Mol Biol. 2491:143-154. ( PubMed )PubMed
154.
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 )PubMed
153.
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 )DOI
152.
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 )DOI
2021
151.
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 )DOI
150.
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 )RSC site
149.
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 )PubMed
148.
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 )PubMed
147.
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 )Nature site
146.
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 )PubMed
145.
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 )PubMed
144.
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 )PubMed
143.
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 )PubMed
142.
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 )PubMed
141.
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 )PubMed
2020
140.
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 )PubMed
139.
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 )PubMed
138.
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 )PubMed
137.
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 )PubMed
136.
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 )PubMed
135.
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 )PubMed
134.
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 )PubMed
133.
Hantschel O, Biancalana M, Koide S. Monobodies as enabling tools for structural and mechanistic biology. Curr Opin Struct Biol. 60:167-174. ( PubMed )PubMed
2019
132.
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 )PubMed
131.
Koide S. Repurposing off-the-shelf antihelix antibodies for enabling structural biology. Proc Natl Acad Sci U S A. 116:17611-17613. ( PubMed )PubMed
130.
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 )PubMed
129.
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 )PubMed
2018
128.
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 )PubMed
127.
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 )PubMed
126.
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)PubMed
125.
Hattori T, Koide S. Next-generation antibodies for post-translational modifications. Curr Opin Struct Biol. 51:141-148. (PubMed)PubMed
124.
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)PubMed
123.
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)PubMed
122.
Diver MM, Pedi L, Koide A, Koide S, Long SB. Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature.553:526-529. (PubMed)PubMed
2017
121.
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)PubMed
120.
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)PubMed
119.
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 )PubMed
118.
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)PubMed
117.
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)PubMed
116.
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)PubMed
115.
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)PubMed
114.
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)PubMed
113.
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)PubMed
112.
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)PubMed
2016
111.
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)PubMed
110.
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)PubMed
109.
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)PubMed
108.
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)PubMedPubMed
2015
107.
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)PubMed
106.
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)PubMed
105.
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)PubMed
104.
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)PubMed
103.
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)PubMed
102.
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) .PubMed
101.
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)PubMed
100.
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)PubMed
99.
Biancalana M, Makabe K, Yan S, Koide S. Aromatic cluster mutations produce focal modulations of β-sheet structure. Protein Sci. 24:841-9. (PubMed)PubMed
2014
98.
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)PubMed
97.
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)PubMed
96.
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)PubMed
95.
Koide S, Kortemme T. Editorial overview: Engineering and design: raising the bar through innovation and integration.Curr Opin Struct Biol. 27:vi-viii. (PubMed)PubMed
94.
93.
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)PubMed
2013
92.
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 .]PubMedFaculty of 1000
91.
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)PubMed
90.
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)PubMed
89.
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 .]PubMedFaculty of 1000
88.
Koide S, Huang J. (2013) Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping. Methods Enzymol. 523:285-302 . (PubMed)PubMed
87.
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 .]PubMedFaculty of 1000
86.
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)PubMed
2012
85.
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)PubMed
84.
Gibreth RN, Koide S. (2012) Structural Insights for Engineering Binding Proteins Based on Non-Antibody Scaffolds. Curr Opin Struct Biol, 22:413-20. (PubMed)PubMed
83.
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)PubMed
82.
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)PubMed
81.
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)PubMed
80.
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)PubMed
79.
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)PubMed
78.
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)PubMed
2011
77.
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)PubMed
76.
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)PubMed
75.
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)PubMed
74.
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)PubMed
73.
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)PubMed
2010
72.
Biancalana M & Koide S. (2010) Molecular mechanism of thioflavin-T binding to peptide self-assemblies. BBA Proteins and Proteomics, 1804, 1405-1412. (PubMed)PubMed
71.
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)PubMed
70.
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)PubMed
69.
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)PubMed
68.
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)PubMed
2009
67.
Koide S. (2009) Generation of novel protein functions by domain combinations and rearrangements. Curr Opin Biotechnol, 20, 398-404. (PubMed)PubMed
66.
Koide S. (2009) Engineering synthetic chaperones for crystallization. Curr Opin Struct Biol, 19, 449-457. (PubMed)PubMed
65.
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)PubMed
64.
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)PubMed
63.
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)PubMed
62.
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)PubMed
61.
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)PubMed
60.
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)PubMed
59.
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)PubMed
58.
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)PubMed
57.
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)PubMed
56.
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)PubMed
2008
55.
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)PubMed
54.
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)PubMed
53.
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)PubMed
52.
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)PubMed
51.
Kossiakoff AA & Koide S. (2008) Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. Curr Opin Struct Biol. 18, 499-506. (PubMed)PubMed
50.
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)PubMed
49.
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)PubMed
48.
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)PubMed
47.
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)PubMed
46.
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)PubMed
2007
45.
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)PubMed
44.
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)PubMed
43.
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)PubMed
42.
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)PubMed
41.
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)PubMed
40.
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)PubMed
39.
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)PubMed
38.
Sidhu SS & Koide S. (2007). Phage display for engineering and analyzing molecular recognition interfaces. Curr Opin Struct Biol, 17, 481-487. (PubMed)PubMed
37.
Koide S. (2007). Minimalist engineering of protein-protein interactions. Chemistry and Biology (Tokyo), 45, 785-791.
2006
36.
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)PubMed
35.
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)PubMed
34.
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)PubMed
33.
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)PubMed
2005
32.
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)PubMed
31.
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)PubMed
30.
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)PubMed
29.
Skafar DF & Koide S. (2006) Understanding the human estrogen receptor-alpha using targeted mutagenesis. Mol Cell Endocrinol 246, 83-90. (PubMed)PubMed
2004
28.
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)PubMed
27.
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)PubMed
26.
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)PubMed
2003
25.
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)PubMed
24.
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)PubMed
23.
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)PubMed
2002
22.
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)PubMed
21.
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)PubMed
20.
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)PubMed
19.
Pawley NH., Koide S. and Nicholson L. (2002) Backbone Dynamics and Thermodynamics of Outer Surface Protein A. J Mol Biol 324, 991-1002. (PubMed)PubMed
18.
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)PubMed
2001
17.
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)PubMed
16.
Yudt MR & Koide S. (2001) Preventing estrogen receptor action with dimer-interface peptides. Steroids 66, 549-558. (PubMed)PubMed
15.
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)PubMed
14.
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)PubMed
13.
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)PubMed
12.
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)PubMed
2000
11.
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)PubMed
10.
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)PubMed
9.
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)PubMed
8.
Ohnishi S & Koide S. (2000) Proteins without a hydrophobic core: structure and stability. Proteins, Nucleic Acids and Enzymes (Tokyo), 45, 2502-2510. (PubMed)PubMed
1999
7.
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)PubMed
6.
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)PubMed
1998
5.
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)PubMed
4.
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)PubMed
3.
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)PubMed
2.
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)PubMed
1.
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)PubMed