메뉴 건너뛰기




Volumn 2009, Issue 3, 2009, Pages 71-81

Automated detection of conformational epitopes using phage display peptide sequences

Author keywords

Conformational epitopes; Peptides; Phage display

Indexed keywords

EPITOPE;

EID: 69849095169     PISSN: None     EISSN: 11779322     Source Type: Journal    
DOI: 10.4137/bbi.s2745     Document Type: Article
Times cited : (78)

References (53)
  • 1
    • 0034235234 scopus 로고    scopus 로고
    • Dominant Epitopes and Allergic Cross-Reactivity: Complex Formation Between a Fab Fragment of a Monoclonal Murine IgG Antibody and the Major Allergen from Birch Pollen Bet v 1
    • Mirza O, Henriksen A, Ipsen H, et al. Dominant Epitopes and Allergic Cross-Reactivity: Complex Formation Between a Fab Fragment of a Monoclonal Murine IgG Antibody and the Major Allergen from Birch Pollen Bet v 1. J Immunol. 2000;165:331-8.
    • (2000) J Immunol , vol.165 , pp. 331-338
    • Mirza, O.1    Henriksen, A.2    Ipsen, H.3
  • 2
    • 34047171268 scopus 로고    scopus 로고
    • Identification of a B-cell Epitope of Hyaluronidase, a Major Bee Venom Allergen, from its Crystal Structure in Complex with a Specific Fab
    • Padavattan S, Schirmer T, Schmidt M, et al. Identification of a B-cell Epitope of Hyaluronidase, a Major Bee Venom Allergen, from its Crystal Structure in Complex with a Specific Fab. Journal of Molecular Biology. 2007;368:742-52.
    • (2007) Journal of Molecular Biology , vol.368 , pp. 742-752
    • Padavattan, S.1    Schirmer, T.2    Schmidt, M.3
  • 3
    • 0029851221 scopus 로고    scopus 로고
    • X-ray crystallography of antibodies
    • Padlan EA. X-ray crystallography of antibodies. Adv Protein Chem. 1996;49:57-133.
    • (1996) Adv Protein Chem , vol.49 , pp. 57-133
    • Padlan, E.A.1
  • 4
    • 0041385755 scopus 로고    scopus 로고
    • Dominating IgE-Binding Epitope of Bet v 1, the Major Allergen of Birch Pollen, Characterized by X-ray Crystallography and Site-Directed Mutagenesis
    • Spangfort MD, Mirza O, Ipsen H, van Neerven RJJ, Gajhede M, Larsen JN. Dominating IgE-Binding Epitope of Bet v 1, the Major Allergen of Birch Pollen, Characterized by X-ray Crystallography and Site-Directed Mutagenesis. J Immunol. 2003;171:3084-90.
    • (2003) J Immunol , vol.171 , pp. 3084-3090
    • Spangfort, M.D.1    Mirza, O.2    Ipsen, H.3    van Neerven, R.J.J.4    Gajhede, M.5    Larsen, J.N.6
  • 5
    • 0038103565 scopus 로고    scopus 로고
    • X-ray snapshots of the maturation of an antibody response to a protein antigen
    • Li Y, Li H, Yang F, Smith-Gill SJ, Mariuzza RA. X-ray snapshots of the maturation of an antibody response to a protein antigen. Nat Struct Mol Biol. 2003;10:482-8.
    • (2003) Nat Struct Mol Biol , vol.10 , pp. 482-488
    • Li, Y.1    Li, H.2    Yang, F.3    Smith-Gill, S.J.4    Mariuzza, R.A.5
  • 6
    • 0037415014 scopus 로고    scopus 로고
    • Exploring protein-protein interactions with phage display
    • Sidhu SS, Fairbrother WJ, Deshayes K. Exploring protein-protein interactions with phage display. Chembiochem. 2003;4:14-25.
    • (2003) Chembiochem , vol.4 , pp. 14-25
    • Sidhu, S.S.1    Fairbrother, W.J.2    Deshayes, K.3
  • 10
    • 0037131408 scopus 로고    scopus 로고
    • Tech.Sight. Phage display. Affinity selection from biological libraries
    • Smothers JF, Henikoff S, Carter P. Tech.Sight. Phage display. Affinity selection from biological libraries. Science. 2002;298:621-2.
    • (2002) Science , vol.298 , pp. 621-622
    • Smothers, J.F.1    Henikoff, S.2    Carter, P.3
  • 11
    • 34249715831 scopus 로고    scopus 로고
    • Full-length antibodies on display
    • Sidhu SS. Full-length antibodies on display. Nat Biotechnol. 2007;25:537-8.
    • (2007) Nat Biotechnol , vol.25 , pp. 537-538
    • Sidhu, S.S.1
  • 13
    • 33748661250 scopus 로고    scopus 로고
    • Computational prediction of the cross-reactive neutralizing epitope corresponding to the monoclonal antibody b12 specific for HIV-1 gp120
    • Bublil E, Yeger-Azuz S, Gershoni J. Computational prediction of the cross-reactive neutralizing epitope corresponding to the monoclonal antibody b12 specific for HIV-1 gp120. FASEB J. 2006;20:1762-74.
    • (2006) FASEB J , vol.20 , pp. 1762-1774
    • Bublil, E.1    Yeger-Azuz, S.2    Gershoni, J.3
  • 15
    • 0033729843 scopus 로고    scopus 로고
    • Allergen mimotopes for 3-dimensional epitope search and induction of antibodies inhibiting human IgE
    • Ganglberger E, Grunberger K, Sponer B, Radauer C, et al. Allergen mimotopes for 3-dimensional epitope search and induction of antibodies inhibiting human IgE. FASEB J. 2000;14:2177-84.
    • (2000) FASEB J , vol.14 , pp. 2177-2184
    • Ganglberger, E.1    Grunberger, K.2    Sponer, B.3    Radauer, C.4
  • 16
    • 20344405720 scopus 로고    scopus 로고
    • 3D-Epitope-Explorer (3DEX): Localization of conformational epitopes within three-dimensional structures of proteins
    • Schreiber A, Humbert M, Benz A, Dietrich U. 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J Comput Chem. 2005;26:879-87.
    • (2005) J Comput Chem , vol.26 , pp. 879-887
    • Schreiber, A.1    Humbert, M.2    Benz, A.3    Dietrich, U.4
  • 17
    • 34249886331 scopus 로고    scopus 로고
    • Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm
    • Bublil E, Freund N, Mayrose I, et al. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins: Structure, Function, and Bioinformatics. 2007;68:294-304.
    • (2007) Proteins: Structure, Function, and Bioinformatics , vol.68 , pp. 294-304
    • Bublil, E.1    Freund, N.2    Mayrose, I.3
  • 18
    • 0142195767 scopus 로고    scopus 로고
    • The Mapping and Reconstitution of a Conformational Discontinuous B-cell Epitope of HIV-1
    • Enshell-Seijffers D, Denisov D, Groisman B, et al. The Mapping and Reconstitution of a Conformational Discontinuous B-cell Epitope of HIV-1. Journal of Molecular Biology. 2003;334:87-101.
    • (2003) Journal of Molecular Biology , vol.334 , pp. 87-101
    • Enshell-Seijffers, D.1    Denisov, D.2    Groisman, B.3
  • 19
    • 0035789124 scopus 로고    scopus 로고
    • New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties
    • Venkatarajan M, Braun W. New quantitative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties. J Mol Model. 2001;7:445-53.
    • (2001) J Mol Model , vol.7 , pp. 445-453
    • Venkatarajan, M.1    Braun, W.2
  • 20
    • 0036772523 scopus 로고    scopus 로고
    • Data mining of sequences and 3D structures of allergenic proteins
    • Ivanciuc O, Schein CH, Braun W. Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics. 2002; 18:1358-64.
    • (2002) Bioinformatics , vol.18 , pp. 1358-1364
    • Ivanciuc, O.1    Schein, C.H.2    Braun, W.3
  • 21
    • 0042093623 scopus 로고    scopus 로고
    • Identifying property based sequence motifs in protein families and superfamilies: Application to DNase-1 related endonucleases
    • Mathura VS, Schein CH, Braun W. Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases. Bioinformatics. 2003;19:1381-90.
    • (2003) Bioinformatics , vol.19 , pp. 1381-1390
    • Mathura, V.S.1    Schein, C.H.2    Braun, W.3
  • 22
    • 34848854803 scopus 로고    scopus 로고
    • Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces
    • Negi SS, Braun W. Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. J Mol Model. 2007;13:1157-67.
    • (2007) J Mol Model , vol.13 , pp. 1157-1167
    • Negi, S.S.1    Braun, W.2
  • 23
    • 33749252782 scopus 로고    scopus 로고
    • Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus
    • Negi SS, Kolokoltsov AA, Schein CH, Davey RA, Braun W. Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus. J Mol Model. 2006;12:921-9.
    • (2006) J Mol Model , vol.12 , pp. 921-929
    • Negi, S.S.1    Kolokoltsov, A.A.2    Schein, C.H.3    Davey, R.A.4    Braun, W.5
  • 24
    • 36949010567 scopus 로고    scopus 로고
    • InterProSurf: A web server for predicting interacting sites on protein surfaces
    • Negi SS, Schein CH, Oezguen N, Power TD, Braun W. InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics. 2007;23:3397-9.
    • (2007) Bioinformatics , vol.23 , pp. 3397-3399
    • Negi, S.S.1    Schein, C.H.2    Oezguen, N.3    Power, T.D.4    Braun, W.5
  • 26
    • 0001528720 scopus 로고    scopus 로고
    • Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules
    • Fraczkiewicz R, Braun W. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J Comp Chem. 1998;19:319.
    • (1998) J Comp Chem , vol.19 , pp. 319
    • Fraczkiewicz, R.1    Braun, W.2
  • 27
    • 2942741136 scopus 로고    scopus 로고
    • Generation of Peptide Mimics of the Epitope Recognized by Trastuzumab on the Oncogenic Protein Her-2/neu
    • Riemer AB, Klinger M, Wagner S, Bernhaus A, et al. Generation of Peptide Mimics of the Epitope Recognized by Trastuzumab on the Oncogenic Protein Her-2/neu. J Immunol. 2004;173:394-401.
    • (2004) J Immunol , vol.173 , pp. 394-401
    • Riemer, A.B.1    Klinger, M.2    Wagner, S.3    Bernhaus, A.4
  • 28
    • 17044427149 scopus 로고    scopus 로고
    • Matching of trastuzumab (Herceptin(R)) epitope mimics onto the surface of Her-2/ neu-a new method of epitope definition
    • Riemer AB, Kraml G, Scheiner O, Zielinski CC, Jensen-Jarolim E. Matching of trastuzumab (Herceptin(R)) epitope mimics onto the surface of Her-2/ neu-a new method of epitope definition. Molecular Immunology. 2005;42:1121-4.
    • (2005) Molecular Immunology , vol.42 , pp. 1121-1124
    • Riemer, A.B.1    Kraml, G.2    Scheiner, O.3    Zielinski, C.C.4    Jensen-Jarolim, E.5
  • 29
    • 34848812600 scopus 로고    scopus 로고
    • Mimotope vaccines: Epitope mimics induce anti-cancer antibodies
    • Riemer AB, Jensen-Jarolim E. Mimotope vaccines: Epitope mimics induce anti-cancer antibodies. Immunology Letters. 2007;113:1-5.
    • (2007) Immunology Letters , vol.113 , pp. 1-5
    • Riemer, A.B.1    Jensen-Jarolim, E.2
  • 30
    • 0037434791 scopus 로고    scopus 로고
    • Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab
    • Cho HS, Mason K, Ramyar KX, et al. Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab. Nature. 2003;421:756-60.
    • (2003) Nature , vol.421 , pp. 756-760
    • Cho, H.S.1    Mason, K.2    Ramyar, K.X.3
  • 31
    • 0042243611 scopus 로고    scopus 로고
    • Peptide decoys selected by phage display block in vitro and in vivo activity of a human anti-FVIII inhibitor
    • Villard S, Lacroix-Desmazes S, Kieber-Emmons T, et al. Peptide decoys selected by phage display block in vitro and in vivo activity of a human anti-FVIII inhibitor. Blood. 2003;102:949-52.
    • (2003) Blood , vol.102 , pp. 949-952
    • Villard, S.1    Lacroix-Desmazes, S.2    Kieber-Emmons, T.3
  • 32
    • 0027319588 scopus 로고
    • Biochemical, immunological, and in vivo functional characterization of B-domain-deleted factor VIII
    • Pittman DD, Alderman EM, Tomkinson KN, Wang JH, Giles AR, Kaufman RJ. Biochemical, immunological, and in vivo functional characterization of B-domain-deleted factor VIII. Blood. 1993;81:2925-35.
    • (1993) Blood , vol.81 , pp. 2925-2935
    • Pittman, D.D.1    Alderman, E.M.2    Tomkinson, K.N.3    Wang, J.H.4    Giles, A.R.5    Kaufman, R.J.6
  • 34
    • 0035412387 scopus 로고    scopus 로고
    • Structure of a factor VIII C2 domain-immunoglobulin G4{kappa} Fab complex: Identification of an inhibitory antibody epitope on the surface of factor VIII
    • Spiegel PC Jr, Jacquemin M, Saint-Remy JMR, Stoddard BL, Pratt KP. Structure of a factor VIII C2 domain-immunoglobulin G4{kappa} Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII. Blood. 2001;98:13-9.
    • (2001) Blood , vol.98 , pp. 13-19
    • Spiegel Jr, P.C.1    Jacquemin, M.2    Saint-Remy, J.M.R.3    Stoddard, B.L.4    Pratt, K.P.5
  • 35
    • 33847101745 scopus 로고    scopus 로고
    • Structural definition of a conserved neutralization epitope on HIV-1 gp120
    • Zhou T, Xu L, Dey B, et al. Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature. 2007;445:732-7.
    • (2007) Nature , vol.445 , pp. 732-737
    • Zhou, T.1    Xu, L.2    Dey, B.3
  • 36
    • 0034482696 scopus 로고    scopus 로고
    • Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates
    • Kwong PD, Wyatt R, Majeed S, et al. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure. 2000;8:1329-39.
    • (2000) Structure , vol.8 , pp. 1329-1339
    • Kwong, P.D.1    Wyatt, R.2    Majeed, S.3
  • 37
    • 33846672181 scopus 로고    scopus 로고
    • Epitope mapping using combinatorial phage-display libraries: A graph-based algorithm
    • Mayrose I, Shlomi T, Rubinstein ND, et al. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Research. 2007;35:69-78.
    • (2007) Nucleic Acids Research , vol.35 , pp. 69-78
    • Mayrose, I.1    Shlomi, T.2    Rubinstein, N.D.3
  • 38
    • 0033106192 scopus 로고    scopus 로고
    • Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab
    • Berthet-Colominas C, Monaco S, Novelli A, Sibaï G, Mallet F, Cusack S, et al. Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab. EMBO J. 1999;18:1124-36.
    • (1999) EMBO J , vol.18 , pp. 1124-1136
    • Berthet-Colominas, C.1    Monaco, S.2    Novelli, A.3    Sibaï, G.4    Mallet, F.5    Cusack, S.6
  • 39
    • 0034436049 scopus 로고    scopus 로고
    • Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24
    • Monaco-Malbet S, Berthet-Colominas C, Novelli A, et al. Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24. Structure. 2000;8:1069-77.
    • (2000) Structure , vol.8 , pp. 1069-1077
    • Monaco-Malbet, S.1    Berthet-Colominas, C.2    Novelli, A.3
  • 40
    • 33646183714 scopus 로고    scopus 로고
    • Mapping a neutralizing epitope on the SARS coronavirus spike protein: Computational prediction based on affinity-selected peptides
    • Tarnovitski N, Matthews LJ, Sui JH, Gershoni JM, Marasco WA. Mapping a neutralizing epitope on the SARS coronavirus spike protein: Computational prediction based on affinity-selected peptides. J Mol Biol. 2006;359:190-201.
    • (2006) J Mol Biol , vol.359 , pp. 190-201
    • Tarnovitski, N.1    Matthews, L.J.2    Sui, J.H.3    Gershoni, J.M.4    Marasco, W.A.5
  • 41
    • 24944498409 scopus 로고    scopus 로고
    • Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor
    • Li F, Li W, Farzan M, Harrison SC. Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor. Science. 2005;309:1864-868.
    • (2005) Science , vol.309 , pp. 1864-1868
    • Li, F.1    Li, W.2    Farzan, M.3    Harrison, S.C.4
  • 42
    • 36549031650 scopus 로고    scopus 로고
    • Pepitope: Epitope mapping from affinity-selected peptides
    • Mayrose I, Penn O, Erez E, et al. Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics. 2007;23:3244-246.
    • (2007) Bioinformatics , vol.23 , pp. 3244-3246
    • Mayrose, I.1    Penn, O.2    Erez, E.3
  • 43
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol. 1998;280:1-9.
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 44
    • 0029109468 scopus 로고
    • Protein-protein interactions: A review of protein dimer structures
    • Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol. 1995;63:31-5.
    • (1995) Prog Biophys Mol Biol , vol.63 , pp. 31-35
    • Jones, S.1    Thornton, J.M.2
  • 45
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. Journal of Molecular Biology. 1997;272:133-43.
    • (1997) Journal of Molecular Biology , vol.272 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 46
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
    • Glaser F, Pupko T, Paz I, et al. ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information. Bioinformatics. 2003;19:163-4.
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3
  • 47
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: A structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth H, Raz R, Schreiber G. ProMate: A structure based prediction program to identify the location of protein-protein binding sites. Journal of Molecular Biology. 2004;338:181-99.
    • (2004) Journal of Molecular Biology , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 48
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucl Acids Res. 2007;35:D301-D3.
    • (2007) Nucl Acids Res , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 49
    • 0021818675 scopus 로고
    • Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface
    • Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 1985;228:1315-7.
    • (1985) Science , vol.228 , pp. 1315-1317
    • Smith, G.P.1
  • 51


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.