Enhanced conformational diversity search of CDR-H3 in antibodies: Role of the first CDR-H3 residue

Proteins: Structure, Function and Genetics

Volumn 37, Issue 4, 1999, Pages 683-696

  Kim, Sun Taek ^a,b   Shirai, Hiroki ^a,c   Nakajima, Nobuyuki ^a   Higo, Junichi ^a   Nakamura, Haruki ^a,d  

^a BIOMOL ENG RESEARCH INSTITUTE   (Japan)

^b Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^c MITSUBISHI TANABE PHARMA CORPORATION   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

Hypervariable region; Immunoglobulin; Loop classification; Loop modeling; Multicanonical molecular dynamics

Indexed keywords

AMINO ACID; ANTIBODY; IMMUNOGLOBULIN F(AB) FRAGMENT;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 0344642583     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<683::AID-PROT17>3.0.CO;2-D     Document Type: Article

References (40)

1. Alzari PM, Lascombe MB, Poljak RJ. Three-dimensional structure of antibodies. Annu Rev Immunol 1988;6:555-580.
2. Padlan EA. Anatomy of the antibody molecule. Mol Immunol 1994;31:169-217.
3. Chothia C, Lesk AM. Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 1987;196:901-917.
4. Chothia C, Lesk AM, Tramontano A, Levitt M, et al. Conformations of immunogloblulin hypervariable regions. Nature 1989;342: 877-883.
5. Chothia C, Lesk AM, Gherardi E, et al. Structural repertoire of the human VH segments. J Mol Biol 1992;227:799-817.
6. Wu S, Cygler M. Conformation of complementary determining region L1 loop in murine IgG λ light chain extends the repertoire of canonical forms. J Mol Biol 1993;229:597-601.
7. Shirai H, Kidera A, Nakamura H. Structural classification of CDR-H3 in antibodies. FEBS Lett 1996;399:1-8.
8. Morea V, Tranmontano A, Rustici M, Chothia C, Lesk A. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol 1998;275:269-294.
9. Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJE. Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J Mol Biol 1998;279: 1193-1210.
10. Bruccoleri RE, Haber E, Novotny J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 1988;335:564-568.
11. Higo J, Collura V, Garnier J. Development of an extended simulated annealing method: application to the modeling of complementary determining regions of immunoglobulins. Biopolymers 1992; 32:33-43.
12. Zheng Q, Rosenfeld R, Delisi C, Kyle DJ. Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci 1994;3:493-506.
13. Martin ACR, Cheetham JC, Rees AR. Modeling antibody hypervariable loops: a combined algorithm. Proc Natl Acad Sci USA 1989;86:9268-9272.
14. Pedersen J, Searle S, Henry A, Rees AR. Antibody modeling: beyond homology. Immunomethods 1992;1:126-136.
15. Mas MT, Smith KC, Yarmush DL, Aisaka K, Fine RM. Modeling the anti-CEA antibody combining site by homology and conformational search. Proteins 1992;14:483-498.
16. Webster DM, Rees AR. Molecular modeling of antibody-combining sites. Methods Mol Biol 1995;51:17-49.
17. Bajorath J, Sheriff S. Comparison of an antibody model with an X-ray structure: the variable fragment of BR96. Proteins 1996;24: 152-157.
18. Nakajima N, Nakamura H, Kidera A. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J Phys Chem B 1997;101:817-824.
19. Shirai H, Nakajima N, Higo J, Kidera A, Nakamura H. Conformational sampling of CDR-H3 in antibody by multicanonical molecular dynamics simulation. J Mol Biol 1998;278:481-496.
20. Nakajima N, Higo J, Kidera A, Nakamura H. Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamic simulation. Chem Phys Lett 1997;278:297-301.
21. Berg BA, Neuhaus T. Multicanonical algorithms for the first order phase transitions. Phys Lett B 1991;267:249-253.
22. Berg BA, Neuhaus T. Multicanonical ensemble: a new approach to simulate first-order phase transitions. Phys Rev Lett 1992;68:9-12.
23. Berg BA, Celik T. A new approach to spin-glass simulations. Phys Rev Lett 1992;69:2292-2295.
24. Lee J. New Monte Carlo algorithm: entropic sampling. Phys Rev Lett 1993;71:211-214.
25. Ferrenberg AM, Swendsen RH. New Monte Carlo technique for studying phase transitions. Phys Rev Lett 1988;61:2635-2638.
26. Hansmann UHE, Okamoto Y. Prediction of peptide conformation by multicanonical algorithm: new approach to the multiple-minima problem. J Comput Chem 1993;14:1333-1338.
27. Okamoto Y, Hansmann UHE. Thermodynamics of helix-coil transitions studied by multicanonical algorithm. J Phys Chem 1995;9: 11276-11287.
28. Kidera A. Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide. Proc Natl Acad Sci USA 1995;92:9886-9889.
29. Schaefer M, Bartels C, Karplus M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol 1998;284:835-848.
30. Bartels C, Stote RH, Karplus M. Characterization of flexible molecules in solution: the RGDW peptide. J Mol Biol 1998;284: 1641-1660.
31. Smith DK, Xue H. Sequence profiles of immunoglobulin and immunoglobulin-like domains. J Mol Biol 1997;274:530-545.
32. Hsieh-Wilson LC, Schultz PG, Stevens RC. Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9 Å resolution. Proc Natl Acad Sci USA 1996;93:5363-5367.
33. Evans SV, Sigurskjold BW, Jennings HJ, et al. Evidence for the extended helical nature of polysaccharide epitopes: the 2.8 Å resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for α-(2→8)-polysialic acid. Biochemistry 1995;34:6737-6744.
34. Kabat EA, Wu TT, Perry HM, Gottesman KS, Foeller C. Sequences of proteins of immunological interest. 5th Edition, U.S. Department of Health and Human Services, Public Health Service, National Institutes of Health (NIH Publication no 91-3242), Bethesda, MD, 1991.
35. Bernstein FC, Koetzle TF, et al. The protein data bank. A computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
36. Morikami K, Nakai T, Kidera A, Saito M, Nakamura H. PRESTO: a vectorized molecular mechanics program for biopolymers. Comput Chem 1992;16:243-248.
37. Weiner SJ, Kollman PA, Nguyen DT, Case DA. An all atoms force field for simulations of proteins and nucleic acids. J Comput Chem 1986;7:230-252.
38. Wilmot CM, Thornton JM. Analysis and prediction of the different types of β-turn in proteins. J Mol Biol 1988;203:221-232.
39. Higo J, Nakajima N, Shirai H, Kidera A, Nakamura H. Two-component multicanonical Monte Carlo method for effective conformation sampling. J Comput Chem 1997;18:2086-2092.
40. Nakajima N. A selectively enhanced multicanonical molecular dynamics method for conformational sampling of peptides in realistic water molecules. Chem Phys Lett 1998;288:319-326.