Stacking and energetic contribution of aromatic islands at the binding interface of antibody proteins

Immunome Research

Volumn 6, Issue SUPPL. 1, 2010, Pages

  Wu, Di ^a,b   Sun, Jing ^a,b   Xu, Tianlei ^a,b   Wang, Shuning ^b   Li, Guoqing ^b   Li, Yixue ^b,c   Cao, Zhiwei ^a,b  

^a TONGJI UNIVERSITY   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN ANTIBODY; TRYPTOPHAN; TYROSINE;

ANTIBODY STRUCTURE; ANTIGEN ANTIBODY COMPLEX; ANTIGEN BINDING; BINDING AFFINITY; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; PROTEIN CONFORMATION; STATISTICAL SIGNIFICANCE;

EID: 77957292138     PISSN: None     EISSN: 17457580     Source Type: Journal    
DOI: 10.1186/1745-7580-6-S1-S1     Document Type: Conference Paper

References (45)

1. High Resolution functional analysis of antibody-antigen interactions. L Jin BM Fendly JA Wells, J. Mol. Biol 1992 226 851 865 10.1016/0022-2836(92) 90636-X 1380563
2. Unusual distributions of amino acids in complementarity-determining (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites. EA Kabat TT Wu H Bilofsky, J. Biol. Chem 1977 252 6609 6616 408353
3. Molecular events during maturation of the immune response to oxazolone. C Berek GM Griffiths C Milstein, Nature 1985 316 412 418 10.1038/316412a0 3927173
4. Somatic evolution of variable region structures during an immune response. L Wysocki T Manser ML Gefter, Proc. Natl. Acad. Sci. U.S.A 1986 83 1847 1851 10.1073/pnas.83.6.1847 3485290
5. Generation of an antibody with enhanced affinity and specificity for its antigen by protein engineering. S Roberts JC Cheetham AR Rees, Nature 1987 328 731 734 10.1038/328731a0 3614380
6. Analysis of antigenic surfaces of proteins. S Lea D Stuart, FASEB J 1995 9 87 93 7821764
7. Immunology. IM Roitt J Brostoff DK Male, London: Mosby Year Book 1996
8. Structure, function and properties of antibody binding sites. IS Mian AR Bradwell AJ Olson, J. Mol. Biol. 1991 217 133 151 10.1016/0022-2836(91)90617-F 1988675
9. Anatomy of the antibody molecule. EA Padlan, Mol. Immunol 1994 31 169 217 10.1016/0161-5890(94)90001-9 8114766
10. Interactions of protein antigens with antibodies. DR Davies GH Cohen, Proc. Natl. Acad. Sci. U.S.A 1996 93 7 12 10.1073/pnas.93.1.7 8552677
11. Studies of protein-protein interfaces, a statistical analysis of the hydrophobic effect. CJ Tsai SL Lin HJ Wolfson R Nussinov, Protein Science 1997 6 1 53 64 10.1002/pro.5560060106 9007976
12. Analysis of protein-protein interaction sites using surface patch. S Jones MJ Thornton, J. Mol. Biol 1997 272 1 121 132 10.1006/jmbi.1997.1234 9299342 (Pubitemid 27395542)
13. Residue frequencies and pairing preferences at protein-protein interfaces. F Glaser DM Steinberg IA Vakser N Ben-Tal, Proteins: Struc. Funct 2001 43 2 89 102 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0. CO;2-H
14. Principles of protein-protein interactions. S Jones JM Thorn, Proc. Natl. Acad. Sci. U.S.A 1996 93 1 13 20 10.1073/pnas.93.1.13 8552589
15. The atomic structure of protein-protein recognition sites. L LoConte C Chothia J Janin, J. Mol. Biol 1999 285 5 2177 2198 10.1006/jmbi.1998.2439 9925793
16. Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. FA Fellouse C Wiesmann SS Sidhu, Proc. Natl. Acad. Sci. U.S.A. 2004 101 12467 12472 10.1073/pnas.0401786101 15306681
17. Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code. FA Fellouse PA Barthelemy RF Kelley SS Sidhu, J. Mol. Biol. 2006 357 100 114 10.1016/j.jmb.2005.11.092 16413576
18. Identification of specificity-determining residues in antibodies. EA Padlan C Abergel JP Tipper, FASEB J. 1995 9 133 139 7821752
19. Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. EJ Sundberg M Urrutia BC Braden J Isern D Tsuchiya BA Fields EL Malchiodi J Tormo FP Schwarz RA Mariuzza, Biochemistry 2000 39 15375 15387 10.1021/bi000704l 11112523
20. Dissection of binding interactions in the complex between the anti-lysozyme antibody HyHEL-63 and its antigen. YL Li M Urrutia SJ Smith-Gill RA Mariuzza, Biochemistry 2003 42 11 22 10.1021/bi020589+ 12515535
21. Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. M Shiroishi K Tsumoco Y Tanaka A Yokota T Nakanishi H Kondo I Kumagai, J. Biol. Chem 2007 282 6783 6791 10.1074/jbc.M605197200 17166830
22. Anatomy of hot spots in protein interfaces. AA Bogan KS Thorn, J. Mol. Biol. 1998 280 1 9 10.1006/jmbi.1998.1843 9653027
23. Unraveling hot spots in binding interfaces: progress and challenges. WL DeLano, Curr. Opin. Struct. Biol 2002 12 14 20 10.1016/S0959-440X(02)00283-X 11839484
24. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. KS Thorn AA Bogan, Bioinformatics 2001 17 284 285 10.1093/bioinformatics/17.3.284 11294795
25. The Protein Data Bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne, Nucleic Acids Res 2000 28 235 242 10.1093/nar/28.1.235 10592235
26. IMGT/3Dstructure-DB and IMGT/StructurealQuery, a database and a tool for immunoglobulin, T-cell receptor and MHC structural data. Q Kaas M Ruiz MP Lefranc, Nucl. Acids. Res. 2004 32 208 D210 10.1093/nar/gkh042
27. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T-cell receptors, MHC, IgSF and MhcSF. F Ehrenmann Q Kaas MP Lefranc, Nucl. Acids. Res. 2010 38 301 D307 10.1093/nar/gkp946
28. Specificity of molecular interactions in transient protein-protein interaction interfaces. KI Cho KY Lee KH Lee DS Kim DH Lee, PROTEINS: Struct. Funct. Bioinformatics 2006 65 593 606 10.1002/prot.21056 (Pubitemid 44583210)
29. The importance of being Tyrosine: Lessons in molecular recognition from minimalist synthetic binding proteins. S Koide SS Sidhu, ACS Chemical Biology 2009 4 325 334 10.1021/cb800314v 19298050
30. Residue solvent accessibilities in the unfolded polypeptide chain. P Zielenkiewicz W Saenger, Biophys. J 1992 63 1483 1486 10.1016/S0006-3495(92) 81746-0 1489908
31. The thermodynamics of DNA structural motifs. J SantaLucia Jr D Hicks, Annu. Rev. Biophys. Biomol. Struct 2004 3 415 440 10.1146/annurev.biophys.32. 110601.141800 (Pubitemid 38829966)
32. Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids. LR Rutledge LS Campbell-Verduyn SD Wetmore, Chemical Physical Letters 2007 444 167 175 10.1016/j.cplett.2007.06.090 (Pubitemid 47198574)
33. Solvent rearrangement in an antigen-antibody interface introduced by site-directed mutagenesis of the antibody combining site. X Ysern BA Fields TN Bhat FA Goldbaum W DallAcqua FP Schwarz RJ Poljak A Mariuzza, J. Mol. Biol. 1994 238 496 500 10.1006/jmbi.1994.1309 8176740
34. VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4A resolution and mutational analysis of the interface. YA Muller Y Chen HW Christinger B Li BC Cunningham HB Lowman AM de Vos, Structuer 1998 6 1153 1167 10.1016/S0969-2126(98)00116-6
35. Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen. Y Chen C Wiesmann G Fuh B Li HW Christinger P McKay AM de Vos HB Lowman, J. Mol. Biol 1999 293 865 881 10.1006/jmbi.1999.3192 10543973
36. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. MP Lefranc C Pommié M Ruiz V Giudicelli E Foulquier L Truong V Thouvenin-Contet G Lefranc, Dev. Comp. Immunol. 2003 27 55 77 10.1016/S0145-305X(02)00039-3 12477501
37. Protein-Ligand binding affinities. MK Gilson HX Zhou, Annu. Rev. Biophys. Biomol. Struct 2007 36 21 42 10.1146/annurev.biophys.36.040306.132550 17201676
38. Free energy calculation-applications to chemical and biochemical phenomena. PA Kollman, Chem Rev 1993 93 2395 2417 10.1021/cr00023a004
39. The statistical-thermodynamic basis for computation of binding affinities: a critical review. MK Gilson JA Given BL Bush JA McCammon, Biophys J 1997 72 1047 1069 10.1016/S0006-3495(97)78756-3 9138555
40. Calculating structures and free eneries of complex molecules: combining molecular mechanics and continuum models. PA Kollman I Massova C Reyes B Kuhn S Huo L Chong M Lee T Lee Y Duan W Wang O Donini P Cieplak J Srinivasan DA Case TE Cheatham III, Acc Chem Res 2000 33 889 897 10.1021/ar000033j 11123888
41. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. JMJ Swanson RH Henchman JA McCammon, Biophys J 2004 86 67 74 10.1016/S0006-3495(04)74084-9 14695250
42. Design of a novel globular protein fold with atomic-level accuracy. B Kuhlman G Dantas GC Ireton G Varani BL Stoddard D Baker, Science 2003 302 1364 1368 10.1126/science.1089427 14631033
43. The interpretation of protein structures: estimation of static accessibility. B Lee FM Richards, J. Mol. Biol. 1971 55 379 400 10.1016/0022-2836(71)90324-X 5551392
44. 'NACCESS', Computer Program. SJ Hubbard JM Thornton, Department of Biochemistry and Molecular Biology, University College London 1993
45. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. S Liu C Zhang H Zhou Y Zhou, Proteins 2004 56 93 101 10.1002/prot.20019 15162489 (Pubitemid 38720841)