메뉴 건너뛰기




Volumn 1824, Issue 3, 2012, Pages 520-532

Antigen-antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures

Author keywords

Computational structural summary of epitopes and paratope; Epitope; Paratope; Protein antigen antibody interface; Specificity of interaction of epitope and paratope amino acid residue

Indexed keywords

EPITOPE;

EID: 84856480671     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2011.12.007     Document Type: Article
Times cited : (138)

References (64)
  • 1
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • DOI 10.1006/jmbi.1998.1943
    • C. Bystroff, and D. Baker Prediction of local structure in proteins using a library of sequence-structure motifs J. Mol. Biol. 281 3 1998 565 577 (Pubitemid 28372132)
    • (1998) Journal of Molecular Biology , vol.281 , Issue.3 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 2
    • 0043222570 scopus 로고    scopus 로고
    • Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA
    • C. Bystroff, and Y. Shao Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA Bioinformatics 18 Suppl 1 2002 S54 S61
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Bystroff, C.1    Shao, Y.2
  • 3
    • 0030779795 scopus 로고    scopus 로고
    • Applying experimental data to protein fold prediction with the genetic algorithm
    • T. Dandekar, and P. Argos Applying experimental data to protein fold prediction with the genetic algorithm Protein Eng. 10 8 1997 877 893 (Pubitemid 27491645)
    • (1997) Protein Engineering , vol.10 , Issue.8 , pp. 877-893
    • Dandekar, T.1    Argos, P.2
  • 4
    • 0042386430 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using pathway models
    • DOI 10.1002/cfg.305
    • X. Yuan, Y. Shao, and C. Bystroff Ab initio protein structure prediction using pathway models Comp. Funct. Genomics 4 4 2003 397 401 (Pubitemid 37098466)
    • (2003) Comparative and Functional Genomics , vol.4 , Issue.4 , pp. 397-401
    • Yuan, X.1    Shao, Y.2    Bystroff, C.3
  • 5
    • 70149112575 scopus 로고    scopus 로고
    • Structural waters define a functional channel mediating activation of the GPCR, rhodopsin
    • T.E. Angel Structural waters define a functional channel mediating activation of the GPCR, rhodopsin Proc. Natl. Acad. Sci. U. S. A. 106 34 2009 14367 14372
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , Issue.34 , pp. 14367-14372
    • Angel, T.E.1
  • 6
    • 0033648564 scopus 로고    scopus 로고
    • Probing protein surface topology by chemical surface labeling, crosslinking, and mass spectrometry
    • K.L. Bennett, T. Matthiesen, and P. Roepstorff Probing protein surface topology by chemical surface labeling, crosslinking, and mass spectrometry Methods Mol. Biol. 146 2000 113 131
    • (2000) Methods Mol. Biol. , vol.146 , pp. 113-131
    • Bennett, K.L.1    Matthiesen, T.2    Roepstorff, P.3
  • 8
    • 47549096059 scopus 로고    scopus 로고
    • Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes
    • DOI 10.1039/b801810c
    • Y. Jin Lee Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes Mol. Biosyst. 4 8 2008 816 823 (Pubitemid 352009216)
    • (2008) Molecular BioSystems , vol.4 , Issue.8 , pp. 816-823
    • Jin Lee, Y.1
  • 12
    • 0022519337 scopus 로고
    • Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution
    • A.G. Amit Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution Science 233 4765 1986 747 753 (Pubitemid 16016225)
    • (1986) Science , vol.233 , Issue.4765 , pp. 747-753
    • Amit, A.G.1    Mariuzza, R.A.2    Phillips, S.E.V.3    Poljak, R.J.4
  • 14
    • 0025964038 scopus 로고
    • Structure, function and properties of antibody binding sites
    • I.S. Mian, A.R. Bradwell, and A.J. Olson Structure, function and properties of antibody binding sites J. Mol. Biol. 217 1 1991 133 151 (Pubitemid 121003282)
    • (1991) Journal of Molecular Biology , vol.217 , Issue.1 , pp. 133-151
    • Mian, I.S.1    Bradwell, A.R.2    Olson, A.J.3
  • 15
    • 0022446684 scopus 로고
    • Continuous and discontinuous protein antigenic determinants
    • D.J. Barlow, M.S. Edwards, and J.M. Thornton Continuous and discontinuous protein antigenic determinants Nature 322 6081 1986 747 748 (Pubitemid 16074126)
    • (1986) Nature , vol.322 , Issue.6081 , pp. 747-748
    • Barlow, D.J.1    Edwards, M.S.2    Thornton, J.M.3
  • 16
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • DOI 10.1006/jmbi.1998.2439
    • L. Lo Conte, C. Chothia, and J. Janin The atomic structure of protein-protein recognition sites J. Mol. Biol. 285 5 1999 2177 2198 (Pubitemid 29078179)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.5 , pp. 2177-2198
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 17
    • 0030174309 scopus 로고    scopus 로고
    • Mapping epitope structure and activity: From one-dimensional prediction to four-dimensional description of antigenic specificity
    • DOI 10.1006/meth.1996.0054
    • M.H.V. Van Regenmortel Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity Methods 9 3 1996 465 472 (Pubitemid 26273467)
    • (1996) Methods: A Companion to Methods in Enzymology , vol.9 , Issue.3 , pp. 465-472
    • Van Regenmortel, M.H.V.1
  • 18
    • 0025151612 scopus 로고
    • Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding
    • T.N. Bhat Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding Nature 347 6292 1990 483 485
    • (1990) Nature , vol.347 , Issue.6292 , pp. 483-485
    • Bhat, T.N.1
  • 19
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • D.D. Boehr, R. Nussinov, and P.E. Wright The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 11 2009 789 796
    • (2009) Nat. Chem. Biol. , vol.5 , Issue.11 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 20
    • 0034732988 scopus 로고    scopus 로고
    • Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63
    • DOI 10.1021/bi000054l
    • Y. Li Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,) Biochemistry 39 21 2000 6296 6309 (Pubitemid 30347133)
    • (2000) Biochemistry , vol.39 , Issue.21 , pp. 6296-6309
    • Li, Y.1    Li, H.2    Smith-Gill, S.J.3    Mariuzza, R.A.4
  • 21
  • 22
    • 79960002053 scopus 로고    scopus 로고
    • Antigenicity and immunogenicity of viral proteins
    • B.W.J. Mahy, M.H.V. Van Regenmortel, Academic Press San Diego
    • M.H. Van Regenmortel Antigenicity and immunogenicity of viral proteins B.W.J. Mahy, M.H.V. Van Regenmortel, Desk Encyclopedia of General Virology 2010 Academic Press San Diego 343 349
    • (2010) Desk Encyclopedia of General Virology , pp. 343-349
    • Van Regenmortel, M.H.1
  • 24
    • 74449089618 scopus 로고    scopus 로고
    • Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes
    • M.B. Irving Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes Mol. Immunol. 47 5 2010 1137 1148
    • (2010) Mol. Immunol. , vol.47 , Issue.5 , pp. 1137-1148
    • Irving, M.B.1
  • 25
    • 0033667160 scopus 로고    scopus 로고
    • Mimotopes: Realization of an unlikely concept
    • R.H. Meloen, W.C. Puijk, and J.W. Slootstra Mimotopes: realization of an unlikely concept J. Mol. Recognit. 13 6 2000 352 359
    • (2000) J. Mol. Recognit. , vol.13 , Issue.6 , pp. 352-359
    • Meloen, R.H.1    Puijk, W.C.2    Slootstra, J.W.3
  • 29
    • 33646150213 scopus 로고    scopus 로고
    • Discontinuous epitope prediction based on mimotope analysis
    • V. Moreau Discontinuous epitope prediction based on mimotope analysis Bioinformatics 22 9 2006 1088 1095
    • (2006) Bioinformatics , vol.22 , Issue.9 , pp. 1088-1095
    • Moreau, V.1
  • 30
    • 60649084396 scopus 로고    scopus 로고
    • Pep-3D-Search: A method for B-cell epitope prediction based on mimotope analysis
    • Y.X. Huang Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis BMC Bioinforma. 9 2008 538
    • (2008) BMC Bioinforma. , vol.9 , pp. 538
    • Huang, Y.X.1
  • 31
    • 80052876042 scopus 로고    scopus 로고
    • MimoPro: A more efficient Web-based tool for epitope prediction using phage display libraries
    • W.H. Chen MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries BMC Bioinforma. 12 2011 199
    • (2011) BMC Bioinforma. , vol.12 , pp. 199
    • Chen, W.H.1
  • 32
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • DOI 10.1006/jmbi.1998.1843
    • A.A. Bogan, and K.S. Thorn Anatomy of hot spots in protein interfaces J. Mol. Biol. 280 1 1998 1 9 (Pubitemid 28312802)
    • (1998) Journal of Molecular Biology , vol.280 , Issue.1 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 33
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • W.L. DeLano Unraveling hot spots in binding interfaces: progress and challenges Curr. Opin. Struct. Biol. 12 1 2002 14 20
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , Issue.1 , pp. 14-20
    • Delano, W.L.1
  • 35
    • 0023953328 scopus 로고
    • Cognitive features of continuous antigenic determinants
    • H.M. Geysen, T.J. Mason, and S.J. Rodda Cognitive features of continuous antigenic determinants J. Mol. Recognit. 1 1 1988 32 41
    • (1988) J. Mol. Recognit. , vol.1 , Issue.1 , pp. 32-41
    • Geysen, H.M.1    Mason, T.J.2    Rodda, S.J.3
  • 37
    • 0030580057 scopus 로고    scopus 로고
    • Antibody-antigen interactions: Contact analysis and binding site topography
    • DOI 10.1006/jmbi.1996.0548
    • R.M. MacCallum, A.C. Martin, and J.M. Thornton Antibody-antigen interactions: contact analysis and binding site topography J. Mol. Biol. 262 5 1996 732 745 (Pubitemid 26343518)
    • (1996) Journal of Molecular Biology , vol.262 , Issue.5 , pp. 732-745
    • MacCallum, R.M.1    Martin, A.C.R.2    Thornton, J.M.3
  • 39
    • 0036420965 scopus 로고    scopus 로고
    • Molecular recognition in antibody-antigen complexes
    • DOI 10.1016/S0065-3233(02)61004-6
    • E.J. Sundberg, and R.A. Mariuzza Molecular recognition in antibody-antigen complexes Adv. Protein Chem. 61 2002 119 160 (Pubitemid 35303456)
    • (2002) Advances in Protein Chemistry , vol.61 , pp. 119-160
    • Sundberg, E.J.1    Mariuzza, R.A.2
  • 40
    • 65649123444 scopus 로고    scopus 로고
    • Structure-activity relationships in peptide-antibody complexes: Implications for epitope prediction and development of synthetic peptide vaccines
    • S.W. Chen, M.H. Van Regenmortel, and J.L. Pellequer Structure-activity relationships in peptide-antibody complexes: implications for epitope prediction and development of synthetic peptide vaccines Curr. Med. Chem. 16 8 2009 953 964
    • (2009) Curr. Med. Chem. , vol.16 , Issue.8 , pp. 953-964
    • Chen, S.W.1    Van Regenmortel, M.H.2    Pellequer, J.L.3
  • 41
    • 0025327474 scopus 로고
    • Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures
    • D. Bordo, and P. Argos Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures J. Mol. Biol. 211 4 1990 975 988 (Pubitemid 20113674)
    • (1990) Journal of Molecular Biology , vol.211 , Issue.4 , pp. 975-988
    • Burdo, D.1    Argos, P.2
  • 42
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • M.F. Sanner, A.J. Olson, and J.C. Spehner Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 3 1996 305 320
    • (1996) Biopolymers , vol.38 , Issue.3 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 43
    • 0036773411 scopus 로고    scopus 로고
    • Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
    • B.J. McConkey, V. Sobolev, and M. Edelman Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure Bioinformatics 18 10 2002 1365 1373 (Pubitemid 35244194)
    • (2002) Bioinformatics , vol.18 , Issue.10 , pp. 1365-1373
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 45
    • 66149137648 scopus 로고    scopus 로고
    • Structural comparison of different antibodies interacting with parvovirus capsids
    • S. Hafenstein Structural comparison of different antibodies interacting with parvovirus capsids J. Virol. 83 11 2009 5556 5566
    • (2009) J. Virol. , vol.83 , Issue.11 , pp. 5556-5566
    • Hafenstein, S.1
  • 46
    • 42449161827 scopus 로고    scopus 로고
    • The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
    • DOI 10.1007/s00018-007-7451-x
    • R.P. Bahadur, and M. Zacharias The interface of protein-protein complexes: analysis of contacts and prediction of interactions Cell Mol. Life Sci. 65 7-8 2008 1059 1072 (Pubitemid 351563896)
    • (2008) Cellular and Molecular Life Sciences , vol.65 , Issue.7-8 , pp. 1059-1072
    • Bahadur, R.P.1    Zacharias, M.2
  • 47
    • 59549088662 scopus 로고    scopus 로고
    • ProtorP: A protein-protein interaction analysis server
    • C. Reynolds, D. Damerell, and S. Jones ProtorP: a protein-protein interaction analysis server Bioinformatics 25 3 2009 413 414
    • (2009) Bioinformatics , vol.25 , Issue.3 , pp. 413-414
    • Reynolds, C.1    Damerell, D.2    Jones, S.3
  • 48
    • 84952503562 scopus 로고
    • 13 ways to look at the correlation-coefficient
    • J.L. Rodgers, and W.A. Nicewander 13 ways to look at the correlation-coefficient Am. Stat. 42 1 1988 59 66
    • (1988) Am. Stat. , vol.42 , Issue.1 , pp. 59-66
    • Rodgers, J.L.1    Nicewander, W.A.2
  • 51
    • 0027413419 scopus 로고
    • Functional importance of amino acid residues making up peptide antigenic determinants
    • C. Pinilla, J.R. Appel, and R.A. Houghten Functional importance of amino acid residues making up peptide antigenic determinants Mol. Immunol. 30 6 1993 577 585
    • (1993) Mol. Immunol. , vol.30 , Issue.6 , pp. 577-585
    • Pinilla, C.1    Appel, J.R.2    Houghten, R.A.3
  • 52
    • 40849097408 scopus 로고    scopus 로고
    • The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies
    • S. Birtalan The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies J. Mol. Biol. 377 5 2008 1518 1528
    • (2008) J. Mol. Biol. , vol.377 , Issue.5 , pp. 1518-1528
    • Birtalan, S.1
  • 53
    • 0025112794 scopus 로고
    • Searching for peptide ligands with an epitope library
    • J.K. Scott, and G.P. Smith Searching for peptide ligands with an epitope library Science 249 4967 1990 386 390
    • (1990) Science , vol.249 , Issue.4967 , pp. 386-390
    • Scott, J.K.1    Smith, G.P.2
  • 54
    • 65749099472 scopus 로고    scopus 로고
    • The importance of being tyrosine: Lessons in molecular recognition from minimalist synthetic binding proteins
    • S. Koide, and S.S. Sidhu The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins ACS Chem. Biol. 4 5 2009 325 334
    • (2009) ACS Chem. Biol. , vol.4 , Issue.5 , pp. 325-334
    • Koide, S.1    Sidhu, S.S.2
  • 55
    • 1842609526 scopus 로고    scopus 로고
    • Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions
    • DOI 10.1016/j.jmb.2004.02.050, PII S002228360400230X
    • S.S. Sidhu Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions J. Mol. Biol. 338 2 2004 299 310 (Pubitemid 38447087)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.2 , pp. 299-310
    • Sidhu, S.S.1    Li, B.2    Chen, Y.3    Fellouse, F.A.4    Eigenbrot, C.5    Fuh, G.6
  • 56
    • 0029016908 scopus 로고
    • Topological mapping of neutrophil cytochrome b epitopes with phage-display libraries
    • J.B. Burritt Topological mapping of neutrophil cytochrome b epitopes with phage-display libraries J. Biol. Chem. 270 28 1995 16974 16980
    • (1995) J. Biol. Chem. , vol.270 , Issue.28 , pp. 16974-16980
    • Burritt, J.B.1
  • 57
    • 0025351555 scopus 로고
    • Epitopes on protein antigens: Misconceptions and realities
    • W.G. Laver Epitopes on protein antigens: misconceptions and realities Cell 61 4 1990 553 556
    • (1990) Cell , vol.61 , Issue.4 , pp. 553-556
    • Laver, W.G.1
  • 58
    • 0038309585 scopus 로고    scopus 로고
    • SiteLight: Binding-site prediction using phage display libraries
    • DOI 10.1110/ps.0237103
    • I. Halperin, H. Wolfson, and R. Nussinov SiteLight: binding-site prediction using phage display libraries Protein Sci. 12 7 2003 1344 1359 (Pubitemid 36759339)
    • (2003) Protein Science , vol.12 , Issue.7 , pp. 1344-1359
    • Halperin, I.1    Wolfson, H.2    Nussinov, R.3
  • 62
    • 84857043317 scopus 로고    scopus 로고
    • Mapping discontinuous antibody epitopes to reveal protein structure and changes in structure related to function
    • B. Mumey Mapping discontinuous antibody epitopes to reveal protein structure and changes in structure related to function Proceedings of the 2003 Ieee Bioinformatics Conference 2003 585 586
    • (2003) Proceedings of the 2003 Ieee Bioinformatics Conference , pp. 585-586
    • Mumey, B.1
  • 63
    • 33750341091 scopus 로고    scopus 로고
    • MIMOX: A web tool for phage display based epitope mapping
    • J. Huang MIMOX: a web tool for phage display based epitope mapping BMC Bioinforma. 7 2006 451
    • (2006) BMC Bioinforma. , vol.7 , pp. 451
    • Huang, J.1
  • 64
    • 20344405720 scopus 로고    scopus 로고
    • 3D-Epitope-Explorer (3DEX): Localization of conformational epitopes within three-dimensional structures of proteins
    • DOI 10.1002/jcc.20229
    • A. Schreiber 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins J. Comput. Chem. 26 9 2005 879 887 (Pubitemid 40860391)
    • (2005) Journal of Computational Chemistry , vol.26 , Issue.9 , pp. 879-887
    • Schreiber, A.1    Humbert, M.2    Benz, A.3    Dietrich, U.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.