An improved model of association for VH-VL immunoglobulin domains: Asymmetries between VH and VL in the packing of some interface residues

Journal of Molecular Recognition

Volumn 16, Issue 3, 2003, Pages 113-120

  Vargas Madrazo, Enrique ^a,b   Paz García, Enrique ^a  

^a UNIVERSIDAD VERACRUZANA   (Mexico)

^b NONE   (Mexico)

Author keywords

Amino acid usage; Antibody engineering; Contact analysis; Diversification strategy; Domain association

Indexed keywords

ANIMALS; BINDING SITES, ANTIBODY; HUMANS; IMMUNOGLOBULIN HEAVY CHAINS; IMMUNOGLOBULIN LIGHT CHAINS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 0038306259     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.613     Document Type: Review

References (38)

1. Alomagro JC, Vargas-Madrazo E, Zenteno-Cuevas R, Hernandez-Mendiola V, Lara-Ochoa F. 1995. VIR: a computational tool for analysis of immunoglobulin sequences. Biosystems 35(1): 25-32.
2. Amzel LM, Poljak RJ. 1979. Three-dimensional structure of immunoglobulins. A. Rev. Biochem. 48: 961-997.
3. 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(2): 161-71.
4. Berek C, Milstein C. 1987. Mutation drift and repertoire shift in the maturation of the immune response. Immunol. Rev. 96: 23-41.
5. Chang CH, Short MT, Westholm FA, Stevens FJ, Wang BC, Furey W Jr, Solomon A, Schiffer M. 1985. Novel arrangement of immunoglobulin variable domains: X-ray crystallographic analysis of the lambda-chain dimer Bence-Jones protein Loc. Biochemistry 24(18): 4890-4897.
6. Chatellier J, Van Regenmortel MH, Vernet T, Altschuh D. 1996. Functional mapping of conserved residues located at the VL and VH domain interface of a Fab. J. Mol. Biol. 264(1): 1-6.
7. Chothia C, Lesk AM. 1987. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196(4): 901-917.
8. Chothia C, Novotny J, Bruccoleri R, Karplus M. 1985. Domain association in immunoglobulin molecules. The packing of variable domains. J. Mol. Biol. 186(3): 651-663.
9. Clackson T, Wells JA. 1995. A hot spot of binding energy in a hormone-receptor interface. Science 267(5196): 383-386.
10. Colman PM. 1988. Structure of antibody-antigen complexes: implications for immune recognition. Adv. Immunol. 43: 99-132.
11. Daugherty PS, Chen G, Iverson BL, Georgiou G. 2000. Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. Proc. Natl. Acad. Sci. USA 97(5): 2029-2034.
12. Davies DR, Metzger H. 1983. Structural basis of antibody function. A. Rev. Immunol. 1: 87-117.
13. Davies DR, Padlan EA, Segal DM. 1975. Three-dimensional structure of immunoglobulins. A. Rev. Biochem. 44: 639-667.
14. Foote J, Winter G. 1992. Antibody framework residues affecting the conformation of the hypervariable loops. J. Mol. Biol. 224(2): 487-499.
15. Hamel PA, Isenman DE, Klein MH, Luedtke R, Dorrington KJ. 1984. Structural basis for the preferential association of autologous immunoglobulin subunits: role of the J region of the light chain. Mol. Immunol. 21(4): 277-283.
16. Honegger A, Pluckthun A. 2001. The influence of the buried glutamine or glutamate residue in position 6 on the structure of immunoglobulin variable domains. J. Mol. Biol. 309(3): 687-699.
17. Jager M, Pluckthun A. 1997. The rate-limiting steps for the folding of an antibody scFv fragment. FEBS Lett. 418(1-2): 106-110.
18. Kabat EA, Wu TT. 1991. Identical V region amino acid sequences and segments of sequences in antibodies of different specificities. Relative contributions of VH and VL genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites. J. Immunol. 147(5): 1709-1719.
19. Khalifa MB, Weidenhaupt M, Choulier L, Chatellier J, Rauffer-Bruyere N, Altschuh D, Vernet T. 2000. Effects on interaction kinetics of mutations at the VH-VL interface of Fabs depend on the structural context. J. Mol. Recognit. 13(3): 127-139.
20. Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM. 1998. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J. Mol. Biol. 275(2): 269-294.
21. Novotny J, Haber E. 1985. Structural invariants of antigen binding: comparison of immunoglobulin VL-VH and VL-VL domain dimers. Proc. Natl. Acad. Sci. USA 82(14): 4592-4596.
22. Novotny J, Bruccoleri R, Newell J, Murphy D, Haber E, Karplus M. 1983. Molecular anatomy of the antibody binding site. J. Biol. Chem. 258(23): 14433-14437.
23. Padlan EA. 1977. Structural basis for the specificity of antibody-antigen reactions and structural mechanisms for the diversification of antigen-binding specificities. Q. Rev. Biophys. 10(1): 35-65.
24. Pokkuluri PR, Huang DB, Raffen R, Cai X, Johnson G, Stevens PW, Stevens FJ, Schiffer M. 1998. A domain flip as a result of a single amino-acid substitution. Structure 6(8): 1067-1073.
25. 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(3): 199-206.
26. Schiffer M, Chang CH, Stevens FJ. 1985. Formation of an infinite β-sheet arrangement dominates the crystallization behavior of lambda-type antibody light chains. J. Mol. Biol. 186(2): 475-478.
27. Schiffer M, Chang CH, Naik VM, Stevens FJ. 1988. Analysis of immunoglobulin domain interactions. Evidence for a dominant role of salt bridges. J. Mol. Biol. 203(3): 799-802.
28. Schillbach JF, Near RI, Bruccoleri RE, Haber E, Jeffrey PD, Novotny J, Sheriff S, Margolies MN. 1993. Modulation of antibody affinity by a non-contact residue. Protein Sci. 2(2): 206-214.
29. Stanfield RL, Takimoto-Kamimura M, Rini JM, Profy AT, Wilson IA. 1993. Major antigen-induced domain rearrangements in an antibody. Structure 1(2): 83-93.
30. Stevens FJ, Chang CH, Schiffer M. 1988. Dual conformations of an immunoglobulin light-chain dimer: heterogeneity of antigen specificity and idiotope profile may result from multiple variable-domain interaction mechanisms. Proc. Natl. Acad. Sci. USA 85(18): 6895-6899.
31. Tomlinson IM, Walter G, Jones PT, Dear PH, Sonnhammer EL, Winter G. 1996. The imprint of somatic hypermutation on the repertoire of human germline V genes. J. Mol. Biol. 256(5): 813-817.
32. Tonegawa S. 1983. Somatic generation of antibody diversity. Nature 302(5909): 575-581.
33. Vargas-Madrazo E, Lara-Ochoa F, Jimenez-Montano M. 1994. A skewed distribution of amino acids at recognition sites of the hypervariable region of immunoglobulins. J. Mol. Evol. 38(1): 100-104.
34. 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(3): 497-504.
35. Wedemayer GJ, Patten PA, Wang LH, Schultz PG, Stevens RC. 1997. Structural insights into the evolution of an antibody combining site. Science 276(5319): 1665-1669.
36. Wiens GD, Roberts VA, Whitcomb EA, O'Hare T, Stenzel-Poore MP, Rittenberg MB. 1998. Harmful somatic mutations: lessons from the dark side. Immunol. Rev. 162: 197-209.
37. Wu TT, Kabat EA. 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(2): 211-250.
38. Wu TT, Johnson G, Kabat EA. 1993. Length distribution of CDRH3 in antibodies. Proteins 16(1): 1-7.