Title:
MOLECULE LIBRARY CONSTRUCTED ON THE BASIS OF BACKBONE STRUCTURE OF MICROPROTEIN
Document Type and Number:
WIPO Patent Application WO/2014/103203
Kind Code:
A1
Abstract:
Disclosed is a molecule library composed of a group of multiple molecules, wherein each member of the library is a polypeptide having a randomized sequence domain and a microprotein domain. The microprotein is a protein that is capable of being folded autonomously in a solution to form a specific three-dimensional conformation and comprises an amino acid sequence composed of 30 or less amino acid residues, such as chignolin that comprises the amino acid sequence represented by SEQ ID NO: 1. Also disclosed is a method for identifying a novel functional molecule using the library of the present invention.
Inventors:
HONDA SHINYA (JP)
WATANABE HIDEKI (JP)
YAMASAKI KAZUHIKO (JP)
WATANABE HIDEKI (JP)
YAMASAKI KAZUHIKO (JP)
Application Number:
PCT/JP2013/007238
Publication Date:
July 03, 2014
Filing Date:
December 09, 2013
Export Citation:
Assignee:
NAT INST OF ADVANCED IND SCIEN (JP)
International Classes:
C40B40/10; C07K7/06; C07K19/00; C12N15/00; C12Q1/68; C40B30/04; C40B40/08; G01N33/53
Domestic Patent References:
| WO1995019374A1 | 1995-07-20 | |||
| WO2000063243A1 | 2000-10-26 |
Foreign References:
| JP2009112282A | 2009-05-28 | |||
| JP2009183292A | 2009-08-20 | |||
| JP2010511691A | 2010-04-15 | |||
| JP2006503088A | 2006-01-26 |
Other References:
CHENG Z. ET AL.: "An engineered tryptophan zipper-type peptide as a molecular recognition scaffold.", J.PEPT.SCI., vol. 15, no. 8, 15 August 2009 (2009-08-15), pages 523 - 532, XP055263606
HERMAN R.E. ET AL.: "The Trp cage motif as a scaffold for the display of a randomized peptide library on bacteriophage T7", J.BIOL.CHEM., vol. 282, no. 13, 30 March 2007 (2007-03-30), pages 9813 - 9824, XP002649241
HIDEKI WATANABE ET AL.: "Bisho Tanpakushitsu o Kozo Kosei Yoso to shita Kogata Jinko ranpakushitsu Sekkei", DAI 13 KAI PROTEIN SCIENCE SOCIETY OF JAPAN NENKAI PROGRAM ยท YOSHISHU, 31 May 2013 (2013-05-31), pages 80, XP008179699
See also references of EP 2940197A4
BONSOR DA; SUNDBERG EJ.: "Dissecting protein-protein interactions using directed evolution", BIOCHEMISTRY, vol. 50, no. 13, 2011, pages 2394 - 402
BINZ HK; AMSTUTZ P; PLUCKTHUN A: "Engineering novel binding proteins from nonimmunoglobulin domains", NAT BIOTECHNOL., vol. 23, 2005, pages 1257 - 1268, XP002381839, DOI: doi:10.1038/nbt1127
HOSSE RJ; ROTHE A; POWER BE: "A new generation of protein display scaffolds for molecular recognition", PROTEIN SCI., vol. 15, 2006, pages 14 - 27, XP002541836, DOI: doi:10.1110/ps.051817606
NILSSON B; MOKS T; JANSSON B; ABRAHMSEN L; ELMBLAD A; HOLMGREN E; HENRICHSON C; JONES TA; UHLEN M: "A synthetic IgG-binding domain based on staphylococcal protein A", PROTEIN ENG., vol. 1, 1987, pages 107 - 113, XP002133892
NORD K; NILSSON J; NILSSON B; UHLEN M; NYGREN PA: "A combinatorial library of an alpha-helical bacterial receptor domain", PROTEIN ENG., vol. 8, 1995, pages 601 - 608
NORD K; GUNNERIUSSON E; RINGDAHL J; STAHL S; UHLEN M; NYGREN PA: "Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain", NAT BIOTECHNOL., vol. 15, 1997, pages 772 - 777
ENGFELDT T; RENBERG B; BRUMER H; NYGREN PA; KARLSTROM AE: "Chemical synthesis of triple-labelled three-helix bundle binding proteins for specific fluorescent detection of unlabelled protein", CHEMBIOCHEM, vol. 6, no. 6, 2005, pages 1043 - 1050, XP055075647, DOI: doi:10.1002/cbic.200400388
TRAN T; ENGFELDT T; ORLOVA A; SANDSTROM M; FELDWISCH J; ABRAHMSEN L; WENNBORG A; TOLMACHEV V; KARLSTROM AE: "99m)Tc-maEEE-Z(HER2:342), an Affibody molecule-based tracer for the detection of HER2 expression in malignant tumors", BIOCONJUG CHEM., vol. 18, no. 6, 2007, pages 1956 - 1964, XP002488608, DOI: doi:10.1021/bc7002617
KOIDE A; BAILEY CW; HUANG X; KOIDE S: "The fibronectin type III domain as a scaffold for novel binding proteins", J MOL BIOL., 1998, pages 1141 - 1151, XP004455886, DOI: doi:10.1006/jmbi.1998.2238
TRAMONTANO A; BIANCHI E; VENTURINI S; MARTIN F; PESSI A; SOLLAZZO M.: "The making of the minibody: an engineered beta-protein for the display of conformationally constrained peptides", J MOL RECOGNIT., vol. 7, 1994, pages 9 - 24
BIANCHI E; VENTURINI S; PESSI A; TRAMONTANO A; SOLLAZZO M: "High level expression and rational mutagenesis of a designed protein, the minibody. From an insoluble to a soluble molecule", J MOL BIOL., vol. 236, no. 2, 1994, pages 649 - 659, XP024008544, DOI: doi:10.1006/jmbi.1994.1174
MCCONNELL SJ; HOESS RH: "Tendamistat as a scaffold for conformationally constrained phage peptide libraries", J MOL BIOL., vol. 250, 1995, pages 460 - 470, XP000985692, DOI: doi:10.1006/jmbi.1995.0390
KU J; SCHULTZ PG: "Alternate protein frameworks for molecular recognition", PROC NATL ACAD SCI USA., vol. 92, 1995, pages 6552 - 6556, XP002923928
QIAN J; LUSCOMBE NM; GERSTEIN M: "Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model", J MOL BIOL., vol. 313, 2001, pages 673 - 681, XP004464236, DOI: doi:10.1006/jmbi.2001.5079
MYSZKA DG; CHAIKEN IM: "Design and characterization of an intramolecular antiparallel coiled coil peptide", BIOCHEMISTRY, vol. 33, 1994, pages 2363 - 2372, XP009191282
1BINZ HK; STUMPP MT; FORRER P; AMSTUTZ P; PLUCKTHUN A: "Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins", J MOL BIOL., vol. 332, 2003, pages 489 - 503, XP027101280, DOI: doi:10.1016/S0022-2836(03)00896-9
SILVERMAN J; LIU Q; BAKKER A; TO W; DUGUAY A; ALBA BM; SMITH R; RIVAS A; LI P; LE H: "Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains", NAT BIOTECHNOL., vol. 23, 2005, pages 1556 - 1561, XP009088629, DOI: doi:10.1038/nbt1166
HUFTON SE; VAN NEER N; VAN DEN BEUKEN T; DESMET J; SABLON E; HOOGENBOOM HR: "Development and application of cytotoxic T lymphocyte-associated antigen 4 as a protein scaffold for the generation of novel binding ligands", FEBS LETT., vol. 475, 2000, pages 225 - 231, XP004337267, DOI: doi:10.1016/S0014-5793(00)01701-4
NELSON AL; REICHERT JM: "Development trends for therapeutic antibody fragments", NAT BIOTECHNOL., vol. 27, no. 4, 2009, pages 331 - 337, XP055295644, DOI: doi:10.1038/nbt0409-331
KNAPPIK A; GE L; HONEGGER A; PACK P; FISCHER M; WELLNHOFER G; HOESS A; WOLLE J; PLUCKTHUN A; VIRNEKAS B: "Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides", J MOL BIOL., vol. 296, no. 1, 2000, pages 57 - 86, XP004461525, DOI: doi:10.1006/jmbi.1999.3444
HONDA, S. YAMASAKI; Y. SAWADA; H. MORII: "10-residue folded peptide designed by segment statistics", STRUCTURE, vol. 12, no. 8, 2004, pages 1507 - 1518, XP025917238, DOI: doi:10.1016/j.str.2004.05.022
HONDA, S.; AKIBA, T.; KATO, Y.S.; SAWADA, Y.; SEKIJIMA, M.; ISHIMURA, M.; OOISHI, A.; WATANABE, H.; ODAHARA, T.; HARATA, K.: "Crystal Structure of a Ten-Amino Acid Protein", J. AM. CHEM. SOC., vol. 130, no. 46, 2008, pages 15327 - 15331
SHINYA HONDA: "Protein'' of 10 amino acids, discovery of chignolin", PROTEIN, NUCLEIC ACID AND ENZYME (PNE, vol. 50, no. 5, 2005, pages 427 - 433
SHINYA HONDA: "Minimal Design of Protein: Structure and wobbling of super chignolin", JOURNAL OF THE BIOPHYSICAL SOCIETY OF JAPAN, vol. 49, no. 3, 2009, pages 126 - 129
NEIDIGH JW; FESINMEYER RM; ANDERSEN NH: "Designing a 20-residue protein", NAT STRUCT BIOL., vol. 9, no. 6, 2002, pages 425 - 430
SARISKY CA; MAYO SL.: "The beta-beta-alpha fold: explorations in sequence space", J MOL BIOL., vol. 307, no. 5, 2001, pages 1411 - 1418, XP002965990, DOI: doi:10.1006/jmbi.2000.4345
NITZ M; SHERAWAT M; FRANZ KJ; PEISACH E; ALLEN KN; IMPERIALI B: "Structural origin of the high affinity of a chemically evolved lanthanide-binding peptide", ANGEW CHEM INT ED ENGL., vol. 43, no. 28, 2004, pages 3682 - 3685, XP002354852, DOI: doi:10.1002/anie.200460028
SEKER UO; DEMIR HV, MOLECULES, vol. 16, no. 2, 2011, pages 1426 - 1451
SEELIG B; SZOSTAK JW: "Selection and evolution of enzymes from a partially randomized non-catalytic scaffold", NATURE, vol. 448, no. 7155, 2007, pages 828 - 831
SALGADO EN; AMBROGGIO XI; BRODIN JD; LEWIS RA; KUHLMAN B; TEZCAN FA: "Metal templated design of protein interfaces", PROC NATL ACAD SCI USA., vol. 107, no. 5, 2010, pages 1827 - 1832
SATOH D; SHIMIZU K; NAKAMURA S; TERADA T.: "Folding free-energy landscape of a 10-residue mini-protein, chignolin", FEBS LETT., vol. 580, no. 14, 2006, pages 3422 - 3426, XP028030647, DOI: doi:10.1016/j.febslet.2006.05.015
XU W; LAI T; YANG Y; MU Y: "Reversible folding simulation by hybrid Hamiltonian replica exchange", J CHEM PHYS., vol. 128, no. 17, 2008, pages 175105
TERADA T; SATOH D; MIKAWA T; ITO Y; SHIMIZU K: "Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation", PROTEINS, vol. 73, no. 3, 2008, pages 621 - 631
ROY S; GOEDECKER S; FIELD MJ; PENEV E.: "A minima hopping study of all-atom protein folding and structure prediction", J PHYS CHEM B, vol. 113, no. 20, 2009, pages 7315 - 7321
HATFIELD MP; MURPHY RF; LOVAS S.: "Molecular dynamics analysis of the conformations of a beta-hairpin miniprotein", J PHYS CHEM B., vol. 114, no. 8, 2010, pages 3028 - 3037
YUZURU FUSHIMI: "Beginning of evolutionary molecular engineering", JOURNAL OF THE BIOPHYSICAL SOCIETY OF JAPAN, vol. 32, 1992, pages 22 - 25
OSAMU OHARA; HISAAKI TANIGUCHI; TETSUO ICHIKAWA; ATSUSHI INUKAI: "Biological High-Performance Equipment - New Technical Manuals", KYORITSU SHUPPAN CO., LTD.
SMITH HO; HUTCHISON CA; PFANNKOCH C; VENTER JC: "Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides", PROC NATL ACAD SCI U S A., vol. 100, no. 26, 2003, pages 15440 - 15445, XP008128718, DOI: doi:10.1073/pnas.2237126100
MULLIS KB; FALOONA FA: "Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction", METHODS ENZYMOL., vol. 155, 1987, pages 335 - 350, XP009003171, DOI: doi:10.1016/0076-6879(87)55023-6
BANER J; NILSSON M; MENDEL-HARTVIG M; LANDEGREN U: "Signal amplification of padlock probes by rolling circle replication", NUCLEIC ACIDS RES., vol. 26, no. 22, 1998, pages 5073 - 5078
NOTOMI T; OKAYAMA H; MASUBUCHI H; YONEKAWA T; WATANABE K; AMINO N; HASE T: "Loop-mediated isothermal amplification of DNA", NUCLEIC ACIDS RES., vol. 28, no. 12, 2000, pages E63, XP003018858, DOI: doi:10.1093/nar/28.12.e63
KEHOE JW; KAY BK: "Filamentous phage display in the new millennium", CHEM REV., vol. 105, no. 11, 2005, pages 4056 - 4072, XP003018054, DOI: doi:10.1021/cr000261r
CICCHINI C; ANSUINI H; AMICONE L; ALONZI T; NICOSIA A; CORTESE R; TRIPODI M; LUZZAGO A: "Searching for DNA-protein interactions by lambda phage display", J MOL BIOL., vol. 322, no. 4, 2002, pages 697 - 706
DANNER S; BELASCO JG: "T7 phage display: a novel genetic selection system for cloning RNA-binding proteins from cDNA libraries", PROC NATL ACAD SCI USA., vol. 98, no. 23, 2001, pages 12954 - 12959, XP002537478, DOI: doi:10.1073/PNAS.211439598
HANES J; PLUCKTHUN A: "In vitro selection and evolution of functional proteins by using ribosome display", PROC NATL ACAD SCI USA., vol. 94, no. 10, 1997, pages 4937 - 4942, XP002079690
WILSON DS; KEEFE AD; SZOSTAK JW: "The use of mRNA display to select high-affinity protein-binding peptides", PROC NATL ACAD SCI USA., vol. 98, no. 7, 2001, pages 3750 - 3755, XP002209215, DOI: doi:10.1073/pnas.061028198
BODER ET; WITTRUP KD: "Yeast surface display for screening combinatorial polypeptide libraries", NAT BIOTECHNOL., vol. 15, no. 6, 1997, pages 553 - 557, XP002945515, DOI: doi:10.1038/nbt0697-553
LU Z; MURRAY KS; VAN CLEAVE V; LAVALLIE ER; STAHL ML; MCCOY JM: "Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin: a system designed for exploring protein-protein interactions", NAT BIOTECHNOLOGY, vol. 13, 1995, pages 366 - 372, XP002033346, DOI: doi:10.1038/nbt0495-366
FIELDS S; SONG O: "A novel genetic system to detect protein-protein interactions", NATURE, vol. 340, no. 6230, 1989, pages 245 - 246, XP000103144, DOI: doi:10.1038/340245a0
WALTER G; BUSSOW K; CAHILL D; LUEKING A; LEHRACH H: "Protein arrays for gene expression and molecular interaction screening", CURR OPIN MICROBIOL., vol. 3, no. 3, 2000, pages 298 - 302, XP000941229, DOI: doi:10.1016/S1369-5274(00)00093-X
RUSMINI F; ZHONG Z; FEIJEN J.: "Protein immobilization strategies for protein biochips", BIOMACROMOLECULES, vol. 8, no. 6, 2007, pages 1775 - 1789
BACKSTROM A; LUNDBERG C; KERSULYTE D; BERG DE; BOREN T; ARNQVIST A: "Metastability of Helicobacter pylori bab adhesin genes and dynamics in Lewis b antigen binding", PROC NATL ACAD SCI USA., vol. 101, no. 48, 2004, pages 16923 - 16928
BEGUM N; HORIUCHI S; TANAKA Y; YAMAMOTO N; ICHIYAMA K; YAMAMOTO N: "New approach for generation of neutralizing antibody against human T-cell leukaemia virus type-I (HTLV-I) using phage clones", VACCINE, vol. 20, no. 9-10, 2002, pages 1281 - 1289, XP004334107, DOI: doi:10.1016/S0264-410X(01)00478-9
KHUEBACHOVA M; VERZILLO V; SKRABANA R; OVECKA M; VACCARO P; PANNI S; BRADBURY A; NOVAK M: "Mapping the C terminal epitope of the Alzheimer's disease specific antibody MN423", J IMMUNOL METHODS, vol. 262, no. 1-2, 2002, pages 205 - 215, XP004352190, DOI: doi:10.1016/S0022-1759(02)00006-6
KRONQVIST N; LOFBLOM J; JONSSON A; WERNERUS H; STAHL S: "A novel affinity protein selection system based on staphylococcal cell surface display and flow cytometry", PROTEIN ENG DES SEL., vol. 21, no. 4, 2008, pages 247 - 255
NOPPE W; PLIEVA F; GALAEV IY; POTTEL H; DECKMYN H; MATTIASSON B: "Chromato-panning: an efficient new mode of identifying suitable ligands from phage display libraries", BMC BIOTECHNOL., vol. 9, 2009, pages 21, XP021049467, DOI: doi:10.1186/1472-6750-9-21
WATANABE H; NAKANISHI T; UMETSU M; KUMAGAI I: "Human anti-gold antibodies: biofunctionalization of gold nanoparticles and surfaces with anti-gold antibodies", J BIOL CHEM., vol. 283, no. 51, 2008, pages 36031 - 36038, XP055220572, DOI: doi:10.1074/jbc.M805547200
FRANCA LT; CARRILHO E; KIST TB: "A review of DNA sequencing techniques", Q REV BIOPHYS, vol. 35, no. 2, 2002, pages 169 - 200, XP009007983, DOI: doi:10.1017/S0033583502003797
SHENDURE J; JI H.: "Next-generation DNA sequencing", NAT BIOTECHNOL., vol. 26, no. 10, 2008, pages 1135 - 1145, XP002572506, DOI: doi:10.1038/nbt1486
KENJI KANGAWA: "Peptides and Drug Discovery", MEDICAL DO
TATSUYA MORIYAMA: "Knowhow of Protein Purification and Handling", YODOSHA CO., LTD
TAIRO OSHIMA; KOICHI SUZUKI; YOSHIAKI FUJII; TAKASHI MURAMATSU: "Post-Sequencing Protein Experiment Methods 3", TOKYO KAGAKU DOZIN CO., LTD.
BRYMORA A; VALOVA VA; ROBINSON PJ: "Protein-protein interactions identified by pulldown experiments and mass spectrometry", CURR PROTOC CELL BIOL., 2004, pages 17
WITTIG I; SCHAGGER H: "Native electrophoretic techniques to identify protein-protein interactions", PROTEOMICS, vol. 9, no. 23, 2009, pages 5214 - 23
PARK SH; RAINES RT: "Fluorescence polarization assay to quantify protein-protein interactions", METHODS MOL BIOL., vol. 261, 2004, pages 161 - 166
FREUND C; ROSS A; GUTH B; PLUCKTHUN A; HOLAK TA: "Characterization of the linker peptide of the single-chain Fv fragment of an antibody by NMR spectroscopy", FEBS LETT., vol. 320, 1993, pages 97 - 100, XP025576238, DOI: doi:10.1016/0014-5793(93)80070-B
IWAKURA M; NAKAMURA T: "Effects of the length of a glycine linker connecting the N-and C- termini of a circularly permuted dihydrofolate reductase", PROTEIN ENG., vol. 11, no. 8, 1998, pages 707 - 713
GUNTERT P; MUMENTHALER C; WUTHRICH K: "Torsion angle dynamics for NMR structure calculation with the new program DYANA", J. MOL. BIOL., vol. 273, 1997, pages 283 - 298, XP004461407, DOI: doi:10.1006/jmbi.1997.1284
DELANO WL; ULTSCH MH; DE VOS AM; WELLS JA: "Convergent solutions to binding at a protein-protein interface", SCIENCE, vol. 287, no. 5456, 2000, pages 1279 - 1283, XP002211313, DOI: doi:10.1126/science.287.5456.1279
DIAS RL; FASAN R; MOEHLE K; RENARD A; OBRECHT D; ROBINSON JA: "Protein ligand design: from phage display to synthetic protein epitope mimetics in human antibody Fc-binding peptidomimetics", J AM CHEM SOC., vol. 128, no. 8, 2006, pages 2726 - 2732, XP008109926, DOI: doi:10.1021/ja057513w
BRUNGER AT; ADAMS PD; CLORE GM; DELANO WL; GROS P; GROSSE-KUNSTLEVE RW; JIANG JS; KUSZEWSKI J; NILGES M; PANNU NS: "Crystallography & NMR system: A new software suite for macromolecular structure determination", ACTA CRYSTALLOGR D BIOL CRYSTALLOGR., vol. 54, 1998, pages 905 - 921
WINN MD; BALLARD CC; COWTAN KD; DODSON EJ; EMSLEY P; EVANS PR; KEEGAN RM; KRISSINEL EB; LESLIE AG; MCCOY A: "Overview of the CCP4 suite and current developments", ACTA CRYSTALLOGR D BIOL CRYSTALLOGR., vol. 67, 2011, pages 235 - 242
EMSLEY P; COWTAN K.: "Coot: model-building tools for molecular graphics", ACTA CRYSTALLOGR D BIOL CRYSTALLOGR., vol. 60, 2004, pages 2126 - 2132
HERMAN R.E. ET AL.: "The Trp cage motif as a scaffold for the display of a randomized peptide library on bacteriophage T7", J.BIOL.CHEM., vol. 282, no. 13, 30 March 2007 (2007-03-30), pages 9813 - 9824, XP002649241
HIDEKI WATANABE ET AL.: "Bisho Tanpakushitsu o Kozo Kosei Yoso to shita Kogata Jinko ranpakushitsu Sekkei", DAI 13 KAI PROTEIN SCIENCE SOCIETY OF JAPAN NENKAI PROGRAM ยท YOSHISHU, 31 May 2013 (2013-05-31), pages 80, XP008179699
See also references of EP 2940197A4
BONSOR DA; SUNDBERG EJ.: "Dissecting protein-protein interactions using directed evolution", BIOCHEMISTRY, vol. 50, no. 13, 2011, pages 2394 - 402
BINZ HK; AMSTUTZ P; PLUCKTHUN A: "Engineering novel binding proteins from nonimmunoglobulin domains", NAT BIOTECHNOL., vol. 23, 2005, pages 1257 - 1268, XP002381839, DOI: doi:10.1038/nbt1127
HOSSE RJ; ROTHE A; POWER BE: "A new generation of protein display scaffolds for molecular recognition", PROTEIN SCI., vol. 15, 2006, pages 14 - 27, XP002541836, DOI: doi:10.1110/ps.051817606
NILSSON B; MOKS T; JANSSON B; ABRAHMSEN L; ELMBLAD A; HOLMGREN E; HENRICHSON C; JONES TA; UHLEN M: "A synthetic IgG-binding domain based on staphylococcal protein A", PROTEIN ENG., vol. 1, 1987, pages 107 - 113, XP002133892
NORD K; NILSSON J; NILSSON B; UHLEN M; NYGREN PA: "A combinatorial library of an alpha-helical bacterial receptor domain", PROTEIN ENG., vol. 8, 1995, pages 601 - 608
NORD K; GUNNERIUSSON E; RINGDAHL J; STAHL S; UHLEN M; NYGREN PA: "Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain", NAT BIOTECHNOL., vol. 15, 1997, pages 772 - 777
ENGFELDT T; RENBERG B; BRUMER H; NYGREN PA; KARLSTROM AE: "Chemical synthesis of triple-labelled three-helix bundle binding proteins for specific fluorescent detection of unlabelled protein", CHEMBIOCHEM, vol. 6, no. 6, 2005, pages 1043 - 1050, XP055075647, DOI: doi:10.1002/cbic.200400388
TRAN T; ENGFELDT T; ORLOVA A; SANDSTROM M; FELDWISCH J; ABRAHMSEN L; WENNBORG A; TOLMACHEV V; KARLSTROM AE: "99m)Tc-maEEE-Z(HER2:342), an Affibody molecule-based tracer for the detection of HER2 expression in malignant tumors", BIOCONJUG CHEM., vol. 18, no. 6, 2007, pages 1956 - 1964, XP002488608, DOI: doi:10.1021/bc7002617
KOIDE A; BAILEY CW; HUANG X; KOIDE S: "The fibronectin type III domain as a scaffold for novel binding proteins", J MOL BIOL., 1998, pages 1141 - 1151, XP004455886, DOI: doi:10.1006/jmbi.1998.2238
TRAMONTANO A; BIANCHI E; VENTURINI S; MARTIN F; PESSI A; SOLLAZZO M.: "The making of the minibody: an engineered beta-protein for the display of conformationally constrained peptides", J MOL RECOGNIT., vol. 7, 1994, pages 9 - 24
BIANCHI E; VENTURINI S; PESSI A; TRAMONTANO A; SOLLAZZO M: "High level expression and rational mutagenesis of a designed protein, the minibody. From an insoluble to a soluble molecule", J MOL BIOL., vol. 236, no. 2, 1994, pages 649 - 659, XP024008544, DOI: doi:10.1006/jmbi.1994.1174
MCCONNELL SJ; HOESS RH: "Tendamistat as a scaffold for conformationally constrained phage peptide libraries", J MOL BIOL., vol. 250, 1995, pages 460 - 470, XP000985692, DOI: doi:10.1006/jmbi.1995.0390
KU J; SCHULTZ PG: "Alternate protein frameworks for molecular recognition", PROC NATL ACAD SCI USA., vol. 92, 1995, pages 6552 - 6556, XP002923928
QIAN J; LUSCOMBE NM; GERSTEIN M: "Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model", J MOL BIOL., vol. 313, 2001, pages 673 - 681, XP004464236, DOI: doi:10.1006/jmbi.2001.5079
MYSZKA DG; CHAIKEN IM: "Design and characterization of an intramolecular antiparallel coiled coil peptide", BIOCHEMISTRY, vol. 33, 1994, pages 2363 - 2372, XP009191282
1BINZ HK; STUMPP MT; FORRER P; AMSTUTZ P; PLUCKTHUN A: "Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins", J MOL BIOL., vol. 332, 2003, pages 489 - 503, XP027101280, DOI: doi:10.1016/S0022-2836(03)00896-9
SILVERMAN J; LIU Q; BAKKER A; TO W; DUGUAY A; ALBA BM; SMITH R; RIVAS A; LI P; LE H: "Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains", NAT BIOTECHNOL., vol. 23, 2005, pages 1556 - 1561, XP009088629, DOI: doi:10.1038/nbt1166
HUFTON SE; VAN NEER N; VAN DEN BEUKEN T; DESMET J; SABLON E; HOOGENBOOM HR: "Development and application of cytotoxic T lymphocyte-associated antigen 4 as a protein scaffold for the generation of novel binding ligands", FEBS LETT., vol. 475, 2000, pages 225 - 231, XP004337267, DOI: doi:10.1016/S0014-5793(00)01701-4
NELSON AL; REICHERT JM: "Development trends for therapeutic antibody fragments", NAT BIOTECHNOL., vol. 27, no. 4, 2009, pages 331 - 337, XP055295644, DOI: doi:10.1038/nbt0409-331
KNAPPIK A; GE L; HONEGGER A; PACK P; FISCHER M; WELLNHOFER G; HOESS A; WOLLE J; PLUCKTHUN A; VIRNEKAS B: "Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides", J MOL BIOL., vol. 296, no. 1, 2000, pages 57 - 86, XP004461525, DOI: doi:10.1006/jmbi.1999.3444
HONDA, S. YAMASAKI; Y. SAWADA; H. MORII: "10-residue folded peptide designed by segment statistics", STRUCTURE, vol. 12, no. 8, 2004, pages 1507 - 1518, XP025917238, DOI: doi:10.1016/j.str.2004.05.022
HONDA, S.; AKIBA, T.; KATO, Y.S.; SAWADA, Y.; SEKIJIMA, M.; ISHIMURA, M.; OOISHI, A.; WATANABE, H.; ODAHARA, T.; HARATA, K.: "Crystal Structure of a Ten-Amino Acid Protein", J. AM. CHEM. SOC., vol. 130, no. 46, 2008, pages 15327 - 15331
SHINYA HONDA: "Protein'' of 10 amino acids, discovery of chignolin", PROTEIN, NUCLEIC ACID AND ENZYME (PNE, vol. 50, no. 5, 2005, pages 427 - 433
SHINYA HONDA: "Minimal Design of Protein: Structure and wobbling of super chignolin", JOURNAL OF THE BIOPHYSICAL SOCIETY OF JAPAN, vol. 49, no. 3, 2009, pages 126 - 129
NEIDIGH JW; FESINMEYER RM; ANDERSEN NH: "Designing a 20-residue protein", NAT STRUCT BIOL., vol. 9, no. 6, 2002, pages 425 - 430
SARISKY CA; MAYO SL.: "The beta-beta-alpha fold: explorations in sequence space", J MOL BIOL., vol. 307, no. 5, 2001, pages 1411 - 1418, XP002965990, DOI: doi:10.1006/jmbi.2000.4345
NITZ M; SHERAWAT M; FRANZ KJ; PEISACH E; ALLEN KN; IMPERIALI B: "Structural origin of the high affinity of a chemically evolved lanthanide-binding peptide", ANGEW CHEM INT ED ENGL., vol. 43, no. 28, 2004, pages 3682 - 3685, XP002354852, DOI: doi:10.1002/anie.200460028
SEKER UO; DEMIR HV, MOLECULES, vol. 16, no. 2, 2011, pages 1426 - 1451
SEELIG B; SZOSTAK JW: "Selection and evolution of enzymes from a partially randomized non-catalytic scaffold", NATURE, vol. 448, no. 7155, 2007, pages 828 - 831
SALGADO EN; AMBROGGIO XI; BRODIN JD; LEWIS RA; KUHLMAN B; TEZCAN FA: "Metal templated design of protein interfaces", PROC NATL ACAD SCI USA., vol. 107, no. 5, 2010, pages 1827 - 1832
SATOH D; SHIMIZU K; NAKAMURA S; TERADA T.: "Folding free-energy landscape of a 10-residue mini-protein, chignolin", FEBS LETT., vol. 580, no. 14, 2006, pages 3422 - 3426, XP028030647, DOI: doi:10.1016/j.febslet.2006.05.015
XU W; LAI T; YANG Y; MU Y: "Reversible folding simulation by hybrid Hamiltonian replica exchange", J CHEM PHYS., vol. 128, no. 17, 2008, pages 175105
TERADA T; SATOH D; MIKAWA T; ITO Y; SHIMIZU K: "Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation", PROTEINS, vol. 73, no. 3, 2008, pages 621 - 631
ROY S; GOEDECKER S; FIELD MJ; PENEV E.: "A minima hopping study of all-atom protein folding and structure prediction", J PHYS CHEM B, vol. 113, no. 20, 2009, pages 7315 - 7321
HATFIELD MP; MURPHY RF; LOVAS S.: "Molecular dynamics analysis of the conformations of a beta-hairpin miniprotein", J PHYS CHEM B., vol. 114, no. 8, 2010, pages 3028 - 3037
YUZURU FUSHIMI: "Beginning of evolutionary molecular engineering", JOURNAL OF THE BIOPHYSICAL SOCIETY OF JAPAN, vol. 32, 1992, pages 22 - 25
OSAMU OHARA; HISAAKI TANIGUCHI; TETSUO ICHIKAWA; ATSUSHI INUKAI: "Biological High-Performance Equipment - New Technical Manuals", KYORITSU SHUPPAN CO., LTD.
SMITH HO; HUTCHISON CA; PFANNKOCH C; VENTER JC: "Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides", PROC NATL ACAD SCI U S A., vol. 100, no. 26, 2003, pages 15440 - 15445, XP008128718, DOI: doi:10.1073/pnas.2237126100
MULLIS KB; FALOONA FA: "Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction", METHODS ENZYMOL., vol. 155, 1987, pages 335 - 350, XP009003171, DOI: doi:10.1016/0076-6879(87)55023-6
BANER J; NILSSON M; MENDEL-HARTVIG M; LANDEGREN U: "Signal amplification of padlock probes by rolling circle replication", NUCLEIC ACIDS RES., vol. 26, no. 22, 1998, pages 5073 - 5078
NOTOMI T; OKAYAMA H; MASUBUCHI H; YONEKAWA T; WATANABE K; AMINO N; HASE T: "Loop-mediated isothermal amplification of DNA", NUCLEIC ACIDS RES., vol. 28, no. 12, 2000, pages E63, XP003018858, DOI: doi:10.1093/nar/28.12.e63
KEHOE JW; KAY BK: "Filamentous phage display in the new millennium", CHEM REV., vol. 105, no. 11, 2005, pages 4056 - 4072, XP003018054, DOI: doi:10.1021/cr000261r
CICCHINI C; ANSUINI H; AMICONE L; ALONZI T; NICOSIA A; CORTESE R; TRIPODI M; LUZZAGO A: "Searching for DNA-protein interactions by lambda phage display", J MOL BIOL., vol. 322, no. 4, 2002, pages 697 - 706
DANNER S; BELASCO JG: "T7 phage display: a novel genetic selection system for cloning RNA-binding proteins from cDNA libraries", PROC NATL ACAD SCI USA., vol. 98, no. 23, 2001, pages 12954 - 12959, XP002537478, DOI: doi:10.1073/PNAS.211439598
HANES J; PLUCKTHUN A: "In vitro selection and evolution of functional proteins by using ribosome display", PROC NATL ACAD SCI USA., vol. 94, no. 10, 1997, pages 4937 - 4942, XP002079690
WILSON DS; KEEFE AD; SZOSTAK JW: "The use of mRNA display to select high-affinity protein-binding peptides", PROC NATL ACAD SCI USA., vol. 98, no. 7, 2001, pages 3750 - 3755, XP002209215, DOI: doi:10.1073/pnas.061028198
BODER ET; WITTRUP KD: "Yeast surface display for screening combinatorial polypeptide libraries", NAT BIOTECHNOL., vol. 15, no. 6, 1997, pages 553 - 557, XP002945515, DOI: doi:10.1038/nbt0697-553
LU Z; MURRAY KS; VAN CLEAVE V; LAVALLIE ER; STAHL ML; MCCOY JM: "Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin: a system designed for exploring protein-protein interactions", NAT BIOTECHNOLOGY, vol. 13, 1995, pages 366 - 372, XP002033346, DOI: doi:10.1038/nbt0495-366
FIELDS S; SONG O: "A novel genetic system to detect protein-protein interactions", NATURE, vol. 340, no. 6230, 1989, pages 245 - 246, XP000103144, DOI: doi:10.1038/340245a0
WALTER G; BUSSOW K; CAHILL D; LUEKING A; LEHRACH H: "Protein arrays for gene expression and molecular interaction screening", CURR OPIN MICROBIOL., vol. 3, no. 3, 2000, pages 298 - 302, XP000941229, DOI: doi:10.1016/S1369-5274(00)00093-X
RUSMINI F; ZHONG Z; FEIJEN J.: "Protein immobilization strategies for protein biochips", BIOMACROMOLECULES, vol. 8, no. 6, 2007, pages 1775 - 1789
BACKSTROM A; LUNDBERG C; KERSULYTE D; BERG DE; BOREN T; ARNQVIST A: "Metastability of Helicobacter pylori bab adhesin genes and dynamics in Lewis b antigen binding", PROC NATL ACAD SCI USA., vol. 101, no. 48, 2004, pages 16923 - 16928
BEGUM N; HORIUCHI S; TANAKA Y; YAMAMOTO N; ICHIYAMA K; YAMAMOTO N: "New approach for generation of neutralizing antibody against human T-cell leukaemia virus type-I (HTLV-I) using phage clones", VACCINE, vol. 20, no. 9-10, 2002, pages 1281 - 1289, XP004334107, DOI: doi:10.1016/S0264-410X(01)00478-9
KHUEBACHOVA M; VERZILLO V; SKRABANA R; OVECKA M; VACCARO P; PANNI S; BRADBURY A; NOVAK M: "Mapping the C terminal epitope of the Alzheimer's disease specific antibody MN423", J IMMUNOL METHODS, vol. 262, no. 1-2, 2002, pages 205 - 215, XP004352190, DOI: doi:10.1016/S0022-1759(02)00006-6
KRONQVIST N; LOFBLOM J; JONSSON A; WERNERUS H; STAHL S: "A novel affinity protein selection system based on staphylococcal cell surface display and flow cytometry", PROTEIN ENG DES SEL., vol. 21, no. 4, 2008, pages 247 - 255
NOPPE W; PLIEVA F; GALAEV IY; POTTEL H; DECKMYN H; MATTIASSON B: "Chromato-panning: an efficient new mode of identifying suitable ligands from phage display libraries", BMC BIOTECHNOL., vol. 9, 2009, pages 21, XP021049467, DOI: doi:10.1186/1472-6750-9-21
WATANABE H; NAKANISHI T; UMETSU M; KUMAGAI I: "Human anti-gold antibodies: biofunctionalization of gold nanoparticles and surfaces with anti-gold antibodies", J BIOL CHEM., vol. 283, no. 51, 2008, pages 36031 - 36038, XP055220572, DOI: doi:10.1074/jbc.M805547200
FRANCA LT; CARRILHO E; KIST TB: "A review of DNA sequencing techniques", Q REV BIOPHYS, vol. 35, no. 2, 2002, pages 169 - 200, XP009007983, DOI: doi:10.1017/S0033583502003797
SHENDURE J; JI H.: "Next-generation DNA sequencing", NAT BIOTECHNOL., vol. 26, no. 10, 2008, pages 1135 - 1145, XP002572506, DOI: doi:10.1038/nbt1486
KENJI KANGAWA: "Peptides and Drug Discovery", MEDICAL DO
TATSUYA MORIYAMA: "Knowhow of Protein Purification and Handling", YODOSHA CO., LTD
TAIRO OSHIMA; KOICHI SUZUKI; YOSHIAKI FUJII; TAKASHI MURAMATSU: "Post-Sequencing Protein Experiment Methods 3", TOKYO KAGAKU DOZIN CO., LTD.
BRYMORA A; VALOVA VA; ROBINSON PJ: "Protein-protein interactions identified by pulldown experiments and mass spectrometry", CURR PROTOC CELL BIOL., 2004, pages 17
WITTIG I; SCHAGGER H: "Native electrophoretic techniques to identify protein-protein interactions", PROTEOMICS, vol. 9, no. 23, 2009, pages 5214 - 23
PARK SH; RAINES RT: "Fluorescence polarization assay to quantify protein-protein interactions", METHODS MOL BIOL., vol. 261, 2004, pages 161 - 166
FREUND C; ROSS A; GUTH B; PLUCKTHUN A; HOLAK TA: "Characterization of the linker peptide of the single-chain Fv fragment of an antibody by NMR spectroscopy", FEBS LETT., vol. 320, 1993, pages 97 - 100, XP025576238, DOI: doi:10.1016/0014-5793(93)80070-B
IWAKURA M; NAKAMURA T: "Effects of the length of a glycine linker connecting the N-and C- termini of a circularly permuted dihydrofolate reductase", PROTEIN ENG., vol. 11, no. 8, 1998, pages 707 - 713
GUNTERT P; MUMENTHALER C; WUTHRICH K: "Torsion angle dynamics for NMR structure calculation with the new program DYANA", J. MOL. BIOL., vol. 273, 1997, pages 283 - 298, XP004461407, DOI: doi:10.1006/jmbi.1997.1284
DELANO WL; ULTSCH MH; DE VOS AM; WELLS JA: "Convergent solutions to binding at a protein-protein interface", SCIENCE, vol. 287, no. 5456, 2000, pages 1279 - 1283, XP002211313, DOI: doi:10.1126/science.287.5456.1279
DIAS RL; FASAN R; MOEHLE K; RENARD A; OBRECHT D; ROBINSON JA: "Protein ligand design: from phage display to synthetic protein epitope mimetics in human antibody Fc-binding peptidomimetics", J AM CHEM SOC., vol. 128, no. 8, 2006, pages 2726 - 2732, XP008109926, DOI: doi:10.1021/ja057513w
BRUNGER AT; ADAMS PD; CLORE GM; DELANO WL; GROS P; GROSSE-KUNSTLEVE RW; JIANG JS; KUSZEWSKI J; NILGES M; PANNU NS: "Crystallography & NMR system: A new software suite for macromolecular structure determination", ACTA CRYSTALLOGR D BIOL CRYSTALLOGR., vol. 54, 1998, pages 905 - 921
WINN MD; BALLARD CC; COWTAN KD; DODSON EJ; EMSLEY P; EVANS PR; KEEGAN RM; KRISSINEL EB; LESLIE AG; MCCOY A: "Overview of the CCP4 suite and current developments", ACTA CRYSTALLOGR D BIOL CRYSTALLOGR., vol. 67, 2011, pages 235 - 242
EMSLEY P; COWTAN K.: "Coot: model-building tools for molecular graphics", ACTA CRYSTALLOGR D BIOL CRYSTALLOGR., vol. 60, 2004, pages 2126 - 2132
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OHNO, Seiji et al. (JP)
Seiji Ono (JP)
Seiji Ono (JP)
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