Koide Laboratory - Publications

2017

  • 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)