Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens

Journal of Molecular Recognition

Volumn 25, Issue 3, 2012, Pages 103-113

  Raghunathan, Gopalan ^a   Smart, Jason ^a   Williams, Joseph ^a   Almagro, Juan Carlos ^b  

^a Centocor Discovery Research   (United States)

^b CENTOCOR INC   (United States)

Author keywords

Complementary determining regions; Hypervariable loops; Immunoglobulins; Somatic mutation; Specificity determining residues

Indexed keywords

ANTIBODY; ANTIGEN;

ALGORITHM; ANIMAL; ANTIBODY AFFINITY; ANTIBODY COMBINING SITE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; HYDROGEN BOND; IMMUNOGLOBULIN VARIABLE REGION; MOUSE; MUTATION; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SURFACE PROPERTY; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; AMINO ACID MOTIFS; ANIMALS; ANTIBODIES; ANTIBODY AFFINITY; ANTIGENS; BINDING SITES, ANTIBODY; CRYSTALLOGRAPHY, X-RAY; HUMANS; HYDROGEN BONDING; IMMUNOGLOBULIN VARIABLE REGION; MICE; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; SURFACE PROPERTIES;

EID: 84863246128     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.2158     Document Type: Article

References (37)

1. Al-Lazikani B, Lesk AM, Chothia C,. 1997. Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273: 927-948. (Pubitemid 27493729)
2. Almagro JC,. 2004. Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires. J. Mol. Recognit. 17: 132-143. (Pubitemid 38370594)
3. Almagro JC, Fransson J,. 2008. Humanization of antibodies. Front. Biosci. 13: 1619-1633. (Pubitemid 351611608)
4. Almagro JC, Quintero-Hernández V, Ortiz-Leõn M, Velandia A, Smith SL, Becerril B,. 2006. Design and validation of a synthetic VH repertoire with tailored diversity for protein recognition. J. Mol. Recognit. 19: 413-422. (Pubitemid 44433820)
5. Amzel L, Poljak R,. 1979. Three-dimensional structure of immunoglobulins. Annu. Rev. Biochem. 48: 961-997. (Pubitemid 10191101)
6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE,. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242. (Pubitemid 30047768)
7. Bond CJ, Wiesmann C, Marsters JCJ, Sidhu SS,. 2005. A structure-based database of antibody variable domain diversity. J. Mol. Biol. 348: 699-709.
8. Capra JD, Kehoe M,. 1974. Variable Region Sequences of Five Human Immunoglobulim Heavy Chains of the VHTTI Subgroup: Definitive Identification of Four Heavy Chain Hypervariable Regions (myeloma proteins/amino acid sequences/antibody combining site). Proc. Natl. Acad. Sci. U. S. A. 71: 845-848.
9. Chothia C, Lesk AM,. 1987. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196: 901-917. (Pubitemid 17127946)
10. Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR, Colman PM, Spinelli S, Alzari PM, Poljak RJ,. 1989. Conformations of immunoglobulin hypervariable regions. Nature 342: 877-883. (Pubitemid 20021331)
11. Chothia C, Lesk AM, Gherardi E, Tomlinson IM, Walter G, Marks JD, Llewelyn MB, Winter G,. 1992. Structural repertoire of the human VH segments. J. Mol. Biol. 227: 799-817.
12. Cobaugh CW, Almagro JC, Pogson M, Iverson B, Georgiou G,. 2008. Synthetic antibody libraries focused towards peptide ligands. J. Mol. Biol. 378: 622-633.
13. Collis AV, Brouwer AP, Martin AC,. 2003. Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. J. Mol. Biol. 325: 337-354. (Pubitemid 36062692)
14. Connolly ML,. 1983. Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709-713.
15. Conte LL, Chothia C, Janin J,. 1999. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285: 2177-2198. (Pubitemid 29078179)
16. Ewert S, Honegger A, Pluckthun A,. 2004. Stability improvement of antibodies for extracellular and intracellular applications: CDR grafting to stable frameworks and structure-based framework engineering. Methods 34: 184-199. (Pubitemid 39092813)
17. Fellouse FA, Li B, Compaan DM, Peden AA, Hymowitz SG, Sidhu SS,. 2005. Molecular recognition by a binary code. J. Mol. Biol. 348: 1153-1162. (Pubitemid 40602373)
18. Fisher RD, Ultsch M, Lingel A, Schaefer G, Shao L, Birtalan S, Sidhu SS, Eigenbrot C,. 2010. Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine. J. Mol. Biol. 402: 217-229.
19. Hoogenboom HR,. 2005. Selecting and screening recombinant antibody libraries. Nat. Biotechnol. 23: 1105-1116. (Pubitemid 41486392)
20. Kaas Q, Ruiz M, Lefranc MP,. 2004. IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res. 32: D208-D210. (Pubitemid 38081640)
21. Kabat EA, Wu TT, Perry HM, Gottesman KS, Foeller C,. 1991. Sequences of proteins of immunological interest, 5th ed. Public Health Service, N.I.H.: Washington. D.C.
22. Lee CV, Liang WC, Dennis MS, Eigenbrot C, Sidhu SS, Fuh G,. 2004. High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J. Mol. Biol. 340: 1073-1093. (Pubitemid 38976491)
23. Lefranc MP, Giudicelli V, Kaas Q, Duprat E, Jabado-Michaloud J, Scaviner D, Ginestoux C, Clement O, Chaume D, Lefranc G,. 2005. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 33: D593-D597. (Pubitemid 40207943)
24. MacCallum R, Martin A, Thornton J,. 1996. Antibody-antigen interactions: contact analysis and binding site topography. J. Mol. Biol. 262: 732-745. (Pubitemid 26343518)
25. Mian IS, Bradwell AR, Olson AJ,. 1991. Structure, function and properties of antibody binding sites. J. Mol. Biol. 217: 133-151. (Pubitemid 121003282)
26. Neuberger MS, Milstein, C,. 1995. Somatic hypermutation. Curr. Opin. Immunol. 7: 248-254.
27. North B, Lehmann A, Dunbrack RL, Jr,. 2011. A new clustering of antibody CDR loop conformations. J. Mol. Biol. 406: 228-256.
28. Padlan E, Abergel C, Tipper J,. 1995. Identification of specificity-determining residues in antibodies. FASEB J. 9: 133-139.
29. Persson H, Lantto J, Ohlin M,. 2006. A focused antibody library for improved hapten recognition. J. Mol. Biol. 357: 607-620. (Pubitemid 43290759)
30. Rajpal A, Beyaz N, Haber L, Cappuccilli G, Yee H, Bhatt RR, Takeuchi T, Lerner RA, Crea R,. 2005. A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc. Natl. Acad. Sci. U. S. A. 102: 8466-8471. (Pubitemid 40862759)
31. Ramirez-Benitez MC, Almagro JC,. 2001. Analysis of antibodies of known structure suggests a lack of correspondence between the residues in contact with the antigen and those modified by somatic hypermutation. Proteins 45: 199-206. (Pubitemid 32990023)
32. Ramirez-Benitez MC, Moreno-Hagelsieb G, Almagro JC,. 2001. VIR.II: a new interface with the antibody sequences in the Kabat database. Biosystems 61: 125-131. (Pubitemid 33051126)
33. Rothe C, Urlinger S, Löhning C, Prassler J, Stark Y, Jäger U, Hubner B, Bardroff M, Pradel I, Boss M, Bittlingmaier R, Bataa T, Frisch C, Brocks B, Honegger A, Urban M,. 2008. The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. J. Mol. Biol. 376: 1182-1200.
34. Shi L, Wheeler JC, Sweet RW, Lu J, Luo J, Tornetta M, Whitaker B, Reddy R, Brittingham R, Borozdina L, Chen Q, Amegadzie B, Knight DM, Almagro JC, Tsui P,. 2010. De novo selection of high affinity antibodies from synthetic antibody libraries displayed on phage as pIX-fusion proteins. J Mol Biol 397: 385-396.
35. Tomlinson IM, Cox JP, Gherardi E, Lesk AM, Chothia C,. 1995. The structural repertoire of the human V kappa domain. EMBO J. 14: 4628-4638.
36. Vargas-Madrazo E, Lara-Ochoa F, Almagro JC,. 1995. Canonical structure repertoire of the antigen-binding site of immunoglobulins suggests strong geometrical restrictions associated to the mechanism of immune recognition. J. Mol. Biol. 254: 497-504. (Pubitemid 26001786)
37. Wilson IA, Ghiara JB, Stanfield RL,. 1994. Structure of anti-peptide antibody complexes. Res. Immunol. 145: 173-178.