References for Koide Lab Technologies

Minimalist interaction interface

  • 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. (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)
  • 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, 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)
  • 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)

Monobody

  • 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)
  • 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)
  • 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)
  • 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, 1141-115. (PubMed)
  • 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, 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • Stockbridge RB, Koide A, Miller C, Koide S.(2014) Proof of dual-topology architecture of Fluc F- channels with monobody blockers. Nat Commun. 5:5120. (PubMed)
  • Tanaka SI, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S.(2015) Monobody-mediated alteration of enzyme specificity. Nat Chem Biol. 11:762-4 (PubMed)
  • Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, Newstead S.(2015) Crystal structures of a double-barrelled fluoride ion channel. Nature. 525:548-51 (PubMed)

Affinity Clamp

  • 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)
  • 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)
  • 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)
  • Koide S. (2009) Generation of novel protein functions by domain combinations and rearrangements. Curr Opin Biotechnol, 20, 398-404. (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)
  • Koide S, Huang J. (2013) Generation of High-Performance Binding Proteins for Peptide Motifs by Affinity Clamping. Methods Enzymol. 523:285-302. (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)

Synthetic Antibody

  • 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)
  • 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)
  • 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)
  • 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)
  • Persson H, Ye W, Wernimont A, Adams JJ, Koide A, Koide S, Lam R, Sidhu SS. (2013) CDR-H3 Diversity Is Not Required for Antigen Recognition by Synthetic Antibodies. J Mol Biol. 425:803-11. (PubMed)
  • 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)
  • 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).

Molecular Display Technology

  • Sidhu SS & Koide S. (2007). Phage display for engineering and analyzing molecular recognition interfaces. Curr Opin Struct Biol, 17, 481-487. (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)
  • 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. *See the Supplementary Materials for detailed descriptions of phage display optimization. (PubMed)

Chaperone-Assisted Structural and Cellular Biology

  • Koide S. (2009) Engineering synthetic chaperones for crystallization. Curr Opin Struct Biol, 19, 449-457. PMC2736338. (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)
  • 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)
  • 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)
  • 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)
  • Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, Newstead S.(2015) Crystal structures of a double-barrelled fluoride ion channel. Nature. 525:548-51 (PubMed)
  • Zhang X, Hoey R, Koide A, Dolios G, Paduch M, Nguyen P, Wu X, Li Y, Wagner SL, Wang R, Koide S, Sisodia SS (2014) Synthetic Antibody Fragment Targeting Nicastrin Affects Assembly and Trafficking of γ-Secretase.J Biol Chem. 289:34851-61. (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)

Antibody Validation

  • 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)
  • 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)
  • Jose CC, Xu B, Jagannathan L, Trac C, Mallela RK, Hattori T, Lai D, Koide S, Schones DE, Cuddapah S. (2014) Epigenetic dysregulation by nickel through repressive chromatin domain disruption.Proc Natl Acad Sci U S A.111:14631-6.(PubMed)