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Volumn 10, Issue 9, 2014, Pages

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGENS; CELL MEMBRANES; T-CELLS;

EID: 84907584667     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003852     Document Type: Article
Times cited : (28)

References (56)
  • 1
    • 0032773506 scopus 로고    scopus 로고
    • The immunoglobulin fold family: sequence analysis and 3D structure comparisons
    • Halaby DM, Poupon A, Mornon J, (1999) The immunoglobulin fold family: sequence analysis and 3D structure comparisons. Protein Eng 12: 563–571.
    • (1999) Protein Eng , vol.12 , pp. 563-571
    • Halaby, D.M.1    Poupon, A.2    Mornon, J.3
  • 2
    • 0023278330 scopus 로고
    • Canonical Structures for the Hypervariable Regions of Immunoglobulins
    • Chothia C, Lesk AM, (1987) Canonical Structures for the Hypervariable Regions of Immunoglobulins. J Mol Biol 196: 901–917.
    • (1987) J Mol Biol , vol.196 , pp. 901-917
    • Chothia, C.1    Lesk, A.M.2
  • 3
    • 0014828908 scopus 로고
    • An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity
    • Wu T, Kabat E, (1970) An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med 132: 211–250.
    • (1970) J Exp Med , vol.132 , pp. 211-250
    • Wu, T.1    Kabat, E.2
  • 4
    • 48049124972 scopus 로고    scopus 로고
    • Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains
    • Abhinandan KR, Martin ACR, (2008) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol Immunol 45: 3832–3839.
    • (2008) Mol Immunol , vol.45 , pp. 3832-3839
    • Abhinandan, K.R.1    Martin, A.C.R.2
  • 5
    • 0025283717 scopus 로고
    • Identification of the region of T cell receptor beta chain that interacts with the self-superantigen MIs-1a
    • Pullen AM, Wade T, Marrack P, Kappler JW, (1990) Identification of the region of T cell receptor beta chain that interacts with the self-superantigen MIs-1a. Cell 61: 1365–1374.
    • (1990) Cell , vol.61 , pp. 1365-1374
    • Pullen, A.M.1    Wade, T.2    Marrack, P.3    Kappler, J.W.4
  • 8
    • 0022339938 scopus 로고
    • Domain Association in Immunoglobulin: The Packing of Variable Domains
    • Chothia C, Novotný J, Bruccoleri R, Karplus M, (1985) Domain Association in Immunoglobulin: The Packing of Variable Domains. J Mol Biol 186: 651–663.
    • (1985) J Mol Biol , vol.186 , pp. 651-663
    • Chothia, C.1    Novotný, J.2    Bruccoleri, R.3    Karplus, M.4
  • 9
    • 0038306259 scopus 로고    scopus 로고
    • An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues
    • Vargas-Madrazo E, Paz-García E, (2003) An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues. J Mol Rec 16: 113–120.
    • (2003) J Mol Rec , vol.16 , pp. 113-120
    • Vargas-Madrazo, E.1    Paz-García, E.2
  • 10
    • 0031253786 scopus 로고    scopus 로고
    • VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs
    • Banfield MJ, King DJ, Mountain A, Brady RL, (1997) VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs. Proteins 29: 161–171.
    • (1997) Proteins , vol.29 , pp. 161-171
    • Banfield, M.J.1    King, D.J.2    Mountain, A.3    Brady, R.L.4
  • 11
    • 80955125900 scopus 로고    scopus 로고
    • Antigen recognition by antibody C836 through adjustment of V L/V H packing
    • Teplyakov A, Obmolova G, Malia T, Gilliland G, (2011) Antigen recognition by antibody C836 through adjustment of V L/V H packing. Acta Crystallogr Sect F 67: 1165–1167.
    • (2011) Acta Crystallogr Sect F , vol.67 , pp. 1165-1167
    • Teplyakov, A.1    Obmolova, G.2    Malia, T.3    Gilliland, G.4
  • 14
    • 77956016509 scopus 로고    scopus 로고
    • Analysis and prediction of VH/VL packing in antibodies
    • Abhinandan KR, Martin ACR, (2010) Analysis and prediction of VH/VL packing in antibodies. Protein Eng Des Sel 23: 689–697.
    • (2010) Protein Eng Des Sel , vol.23 , pp. 689-697
    • Abhinandan, K.R.1    Martin, A.C.R.2
  • 15
    • 79961022281 scopus 로고    scopus 로고
    • The association of heavy and light chain variable domains in antibodies: implications for antigen specificity
    • Chailyan A, Marcatili P, Tramontano A, (2011) The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. FEBS 278: 2858–2866.
    • (2011) FEBS , vol.278 , pp. 2858-2866
    • Chailyan, A.1    Marcatili, P.2    Tramontano, A.3
  • 16
    • 84885010253 scopus 로고    scopus 로고
    • ABangle: characterising the VH-VL orientation in antibodies
    • Dunbar J, Fuchs A, Shi J, Deane CM, (2013) ABangle: characterising the VH-VL orientation in antibodies. Protein Eng Des Sel 24: 611–620.
    • (2013) Protein Eng Des Sel , vol.24 , pp. 611-620
    • Dunbar, J.1    Fuchs, A.2    Shi, J.3    Deane, C.M.4
  • 17
    • 59449096415 scopus 로고    scopus 로고
    • Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking
    • Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ, (2009) Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins 74: 497–514.
    • (2009) Proteins , vol.74 , pp. 497-514
    • Sivasubramanian, A.1    Sircar, A.2    Chaudhury, S.3    Gray, J.J.4
  • 19
    • 0028922319 scopus 로고
    • Chemistry of peptides associated with MHC class I and class II molecules
    • Rammensee HG, (1995) Chemistry of peptides associated with MHC class I and class II molecules. Curr Opin Immunol 7: 85–96.
    • (1995) Curr Opin Immunol , vol.7 , pp. 85-96
    • Rammensee, H.G.1
  • 23
    • 84867432034 scopus 로고    scopus 로고
    • Structural basis for self-recognition by autoimmune T-cell receptors
    • Yin Y, Li Y, Mariuzza Ra, (2012) Structural basis for self-recognition by autoimmune T-cell receptors. Immunol Rev 250: 32–48.
    • (2012) Immunol Rev , vol.250 , pp. 32-48
    • Yin, Y.1    Li, Y.2    Mariuzza, R.3
  • 24
    • 70449470318 scopus 로고    scopus 로고
    • Structural alterations in peptide–MHC recognition by self-reactive T cell receptors
    • Wucherpfennig K, Call M, (2009) Structural alterations in peptide–MHC recognition by self-reactive T cell receptors. Curr Opin Immunol 21: 590–595.
    • (2009) Curr Opin Immunol , vol.21 , pp. 590-595
    • Wucherpfennig, K.1    Call, M.2
  • 25
    • 84859068537 scopus 로고    scopus 로고
    • T-cell-receptor-like antibodies - generation, function and applications
    • Dahan R, Reiter Y, (2012) T-cell-receptor-like antibodies - generation, function and applications. Exp Rev Mol Med 14: e6.
    • (2012) Exp Rev Mol Med , vol.14 , pp. e6
    • Dahan, R.1    Reiter, Y.2
  • 26
    • 84907585592 scopus 로고    scopus 로고
    • T-Cell Receptor-Like Antibodies: Targeting the Intracellular Proteome Therapeutic Potential and Clinical Applications
    • Cohen M, Reiter Y, (2013) T-Cell Receptor-Like Antibodies: Targeting the Intracellular Proteome Therapeutic Potential and Clinical Applications. Antibodies 2: 517–534.
    • (2013) Antibodies , vol.2 , pp. 517-534
    • Cohen, M.1    Reiter, Y.2
  • 28
    • 68249153739 scopus 로고    scopus 로고
    • Fab antibodies capable of blocking T cells by competitive binding have the identical specificity but a higher affinity to the MHC-peptide-complex than the T cell receptor
    • Neumann F, Sturm C, Hülsmeyer M, Dauth N, Guillaume P, et al. (2009) Fab antibodies capable of blocking T cells by competitive binding have the identical specificity but a higher affinity to the MHC-peptide-complex than the T cell receptor. Immunology letters 125: 86–92.
    • (2009) Immunology letters , vol.125 , pp. 86-92
    • Neumann, F.1    Sturm, C.2    Hülsmeyer, M.3    Dauth, N.4    Guillaume, P.5
  • 29
    • 84877057389 scopus 로고    scopus 로고
    • Pharmacokinetics, pharmacodynamics and physiologically-based pharmacokinetic modelling of monoclonal antibodies
    • Dostalek M, Gardner I, Gurbaxani BM, Rose RH, Chetty M, (2013) Pharmacokinetics, pharmacodynamics and physiologically-based pharmacokinetic modelling of monoclonal antibodies. Clin Pharmacokinet 52: 83–124.
    • (2013) Clin Pharmacokinet , vol.52 , pp. 83-124
    • Dostalek, M.1    Gardner, I.2    Gurbaxani, B.M.3    Rose, R.H.4    Chetty, M.5
  • 30
    • 0029962226 scopus 로고    scopus 로고
    • A recombinant antibody with the antigen-specific, major histocompatibility complex-restricted specificity of T cells
    • Andersen PS, Stryhn a, Hansen BE, Fugger L, Engberg J, et al. (1996) A recombinant antibody with the antigen-specific, major histocompatibility complex-restricted specificity of T cells. Proc Natl Acad Sci U S A 93: 1820–1824.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 1820-1824
    • Andersen, P.S.1    Stryhn, A.2    Hansen, B.E.3    Fugger, L.4    Engberg, J.5
  • 31
    • 0141872929 scopus 로고    scopus 로고
    • Recombinant antibodies with MHC-restricted, new tools to study antigen presentation and TCR- peptide-MHC interactions
    • Cohen CJ, Denkberg G, Lev A, Epel M, Reiter Y, (2003) Recombinant antibodies with MHC-restricted, new tools to study antigen presentation and TCR- peptide-MHC interactions. J Mol Recognit 16: 324–332.
    • (2003) J Mol Recognit , vol.16 , pp. 324-332
    • Cohen, C.J.1    Denkberg, G.2    Lev, A.3    Epel, M.4    Reiter, Y.5
  • 32
    • 0042333429 scopus 로고    scopus 로고
    • Tax and M1 Peptide/HLA-A2-Specific Fabs and T Cell Receptors Recognize Nonidentical Structural Features on Peptide/HLA-A2 Complexes
    • Biddison WE, Turner RV, Gagnon SJ, Lev a, Cohen CJ, et al. (2003) Tax and M1 Peptide/HLA-A2-Specific Fabs and T Cell Receptors Recognize Nonidentical Structural Features on Peptide/HLA-A2 Complexes. J Immunol 171: 3064–3074.
    • (2003) J Immunol , vol.171 , pp. 3064-3074
    • Biddison, W.E.1    Turner, R.V.2    Gagnon, S.J.3    Lev, A.4    Cohen, C.J.5
  • 34
    • 19944430890 scopus 로고    scopus 로고
    • A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3
    • Hülsmeyer M, Chames P, Hillig RC, Stanfield RL, Held G, et al. (2005) A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3. J Biol Chem 280: 2972–2980.
    • (2005) J Biol Chem , vol.280 , pp. 2972-2980
    • Hülsmeyer, M.1    Chames, P.2    Hillig, R.C.3    Stanfield, R.L.4    Held, G.5
  • 35
    • 7244240852 scopus 로고    scopus 로고
    • Antibody specific for the peptide.major histocompatibility complex. Is it T cell receptor-like?
    • Mareeva T, Lebedeva T, Anikeeva N, Manser T, Sykulev Y, (2004) Antibody specific for the peptide.major histocompatibility complex. Is it T cell receptor-like? J Biol Chem 279: 44243–44249.
    • (2004) J Biol Chem , vol.279 , pp. 44243-44249
    • Mareeva, T.1    Lebedeva, T.2    Anikeeva, N.3    Manser, T.4    Sykulev, Y.5
  • 36
    • 37549038674 scopus 로고    scopus 로고
    • A New Twist In TCR Diversity Revealed By A Forbidden αβ TCR
    • McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, et al. (2008) A New Twist In TCR Diversity Revealed By A Forbidden αβ TCR. J Mol Biol 375: 1306–1319.
    • (2008) J Mol Biol , vol.375 , pp. 1306-1319
    • McBeth, C.1    Seamons, A.2    Pizarro, J.C.3    Fleishman, S.J.4    Baker, D.5
  • 39
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658–1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 41
    • 75549091258 scopus 로고    scopus 로고
    • IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF
    • Ehrenmann F, Kaas Q, Lefranc M-P, (2010) IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res 38: D301–307.
    • (2010) Nucleic Acids Res , vol.38 , pp. D301-307
    • Ehrenmann, F.1    Kaas, Q.2    Lefranc, M.-P.3
  • 43
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: freely available Python tools for computational molecular biology and bioinformatics
    • Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422–1423.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.A.1    Antao, T.2    Chang, J.T.3    Chapman, B.A.4    Cox, C.J.5
  • 45
    • 84915787472 scopus 로고    scopus 로고
    • Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study
    • Knapp B, Dunbar J, Deane CM, (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. Plos Comp Bio In Press.
    • (2014) Plos Comp Bio
    • Knapp, B.1    Dunbar, J.2    Deane, C.M.3
  • 46
    • 57649165426 scopus 로고    scopus 로고
    • How a T cell receptor-like antibody recognizes major histocompatibility complex-bound peptide
    • Mareeva T, Martinez-Hackert E, Sykulev Y, (2008) How a T cell receptor-like antibody recognizes major histocompatibility complex-bound peptide. J Biol Chem 283: 29053–29059.
    • (2008) J Biol Chem , vol.283 , pp. 29053-29059
    • Mareeva, T.1    Martinez-Hackert, E.2    Sykulev, Y.3
  • 47
    • 0035846910 scopus 로고    scopus 로고
    • T cell receptor-MHC interactions up close
    • Hennecke J, Wiley DC, (2001) T cell receptor-MHC interactions up close. Cell 104: 1–4.
    • (2001) Cell , vol.104 , pp. 1-4
    • Hennecke, J.1    Wiley, D.C.2
  • 48
    • 0037240790 scopus 로고    scopus 로고
    • A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity
    • Kjer-Nielsen L, Clements CS, Purcell AW, Brooks AG, Whisstock JC, et al. (2003) A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity. Immunity 18: 53–64.
    • (2003) Immunity , vol.18 , pp. 53-64
    • Kjer-Nielsen, L.1    Clements, C.S.2    Purcell, A.W.3    Brooks, A.G.4    Whisstock, J.C.5
  • 49
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • Krivov GG, Shapovalov MV, Dunbrack RL, (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77: 778–795.
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack, R.L.3
  • 50
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    • Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375–383.
    • (2007) Nucleic Acids Res , vol.35 , pp. W375-383
    • Davis, I.W.1    Leaver-Fay, A.2    Chen, V.B.3    Block, J.N.4    Kapral, G.J.5
  • 51
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen M-Y, Sali A, (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15: 2507–2524.
    • (2006) Protein Sci , vol.15 , pp. 2507-2524
    • Shen, M.-Y.1    Sali, A.2
  • 52
    • 84862700907 scopus 로고    scopus 로고
    • Disease-associated polyglutamine stretches in monomeric huntingtin adopt a compact structure
    • Peters-Libeu C, Miller J, Rutenber E, Newhouse Y, Krishnan P, et al. (2012) Disease-associated polyglutamine stretches in monomeric huntingtin adopt a compact structure. J Mol Biol 421: 587–600.
    • (2012) J Mol Biol , vol.421 , pp. 587-600
    • Peters-Libeu, C.1    Miller, J.2    Rutenber, E.3    Newhouse, Y.4    Krishnan, P.5
  • 53
    • 79957860276 scopus 로고    scopus 로고
    • In: Kontermann R, Dübel S, editors, 2 ed. Berlin, Heidelberg: Springer Berlin Heidelberg
    • Martin ACR (2010) Antibody Engineering Vol. 2. In: Kontermann R, Dübel S, editors. Antibody Engineering. 2 ed. Berlin, Heidelberg: Springer Berlin Heidelberg. pp. 33–51.
    • (2010) Antibody Engineering , pp. 33-51
    • Martin, A.C.R.1
  • 54
    • 23744479535 scopus 로고    scopus 로고
    • How the T cell receptor sees antigen–a structural view
    • Garcia KC, Adams EJ, (2005) How the T cell receptor sees antigen–a structural view. Cell 122: 333–336.
    • (2005) Cell , vol.122 , pp. 333-336
    • Garcia, K.C.1    Adams, E.J.2
  • 55
    • 62549102995 scopus 로고    scopus 로고
    • TCR-MHC docking orientation: natural selection, or thymic selection?
    • Collins EJ, Riddle DS, (2008) TCR-MHC docking orientation: natural selection, or thymic selection? Immunologic research 41: 267–294.
    • (2008) Immunologic research , vol.41 , pp. 267-294
    • Collins, E.J.1    Riddle, D.S.2
  • 56
    • 84905112393 scopus 로고    scopus 로고
    • T cell receptor bias for MHC: co-evolution or co-receptors?
    • Rangarajan S, Mariuzza Ra, (2014) T cell receptor bias for MHC: co-evolution or co-receptors? Cell Mol Life Sci 71: 3059–3068.
    • (2014) Cell Mol Life Sci , vol.71 , pp. 3059-3068
    • Rangarajan, S.1    Mariuzza, R.2


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