Free energy perturbation approach for the rational engineering of the antibody for human hepatitis B virus

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 5, 2011, Pages 643-649

  Park, Hwangseo ^a   Jeon, Young Ho ^b,c  

^a Sejong University   (South Korea)

^b Korea Basic Science Institute (KBSI)   (South Korea)

^c University of Science and Technology (UST)   (South Korea)

Author keywords

Antibody engineering; Free energy perturbation; Molecular dynamics; Mutation; Protein protein interaction

Indexed keywords

ANTIBODY ENGINEERING; ANTIBODY-ANTIGEN; ANTIBODY-ANTIGEN INTERACTIONS; BINDING AFFINITIES; COMPUTATIONAL TOOLS; DYNAMIC STABILITY; EXPERIMENTAL DATA; FEP CALCULATIONS; FREE ENERGY PERTURBATION; HEPATITIS B VIRUS; HUMANIZED MONOCLONAL ANTIBODY; MOLECULAR DYNAMIC SIMULATIONS; MUTANT ANTIBODIES; MUTATION; PROTEIN CONFORMATION; PROTEIN-PROTEIN INTERACTION; RELATIVE BINDING; SIMULATION STUDIES; SQUARED CORRELATION COEFFICIENTS; STRUCTURAL FEATURE; TRANSLATIONAL MOTIONS; WILD TYPES;

ANTIGENS; ENGINEERING; FREE ENERGY; MOLECULAR DYNAMICS; MONOCLONAL ANTIBODIES; PROTEINS; VIRUSES;

BINDING ENERGY;

ANTIGEN; VIRUS ANTIBODY;

ANTIBODY ENGINEERING; ANTIGEN ANTIBODY COMPLEX; ARTICLE; BINDING AFFINITY; ENERGY TRANSFER; FREE ENERGY PERTUBATION; HEPATITIS B VIRUS; HUMAN; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN INTERACTION;

ANIMALS; ANTIBODIES, MONOCLONAL; COMPUTER SIMULATION; HEPATITIS B VIRUS; HUMANS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEIN ENGINEERING; THERMODYNAMICS;

HEPATITIS B VIRUS;

EID: 79751526644     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.11.010     Document Type: Article

References (24)

1. B. Rehermann, and M. Nascimbeni Immunology of hepatitis B virus and hepatitis C virus infection Nat. Rev. Immunol. 5 2005 215 229 (Pubitemid 40364823)
2. K.H. Heermann, U. Goldmann, W. Schwartz, T. Seyffarth, H. Baumgarten, and W.H. Gerlich Large surface proteins of hepatitis B virus containing the pre-S sequence J. Virol. 52 1984 396 402 (Pubitemid 15202474)
3. M. Nassal Hepatitis B viruses: reverse transcription a different way Virus Res. 134 2008 235 249
4. S. De Falco, M.G. Ruvoletto, A. Verdoliva, M. Ruvo, A. Raucci, M. Marino, S. Senatore, G. Cassani, A. Alberti, P. Pontisso, and G. Fassina Cloning and expression of a novel hepatitis B virus-binding protein from HepG2 cells J. Biol. Chem. 276 2001 36613 36623
5. C.Y. Maeng, C.J. Ryu, P. Gripon, C. Guguen-Guillouzo, and H.J. Hong Fine mapping of virus-neutralizing epitopes on hepatitis B virus preS1 Virology 270 2000 9 16 (Pubitemid 30256535)
6. H.J. Hong, C.J. Ryu, H. Hur, S. Kim, H.K. Oh, M.S. Oh, and S.Y. Park In vivo neutralization of hepatitis B virus infection by an anti-preS1 humanized antibody in chimpanzees Virology 318 2004 134 141 (Pubitemid 38234268)
7. M. Verhoeyen, C. Milstein, and G. Winter Reshaping human antibodies: grafting an antilysozyme activity Science 239 1988 1534 1536
8. S. Stephens, S. Emtage, O. Vetterlein, L. Chaplin, C. Bebbington, A. Nesbitt, M. Sopwith, D. Athwal, C. Novak, and M. Bodmer Comprehensive pharmacokinetics of a humanized antibody and analysis of residual anti-idiotypic responses Immunology 85 1995 668 674
9. L. Riechmann, M. Clark, H. Waldmann, and G. Winter Reshaping human antibodies for therapy Nature 332 1988 323 327 (Pubitemid 18091075)
10. M.S. Co, M. Deschamps, B.J. Whitley, and C. Queen Humanized antibodies for antiviral therapy Proc. Natl. Acad. Sci. U.S.A. 88 1991 2869 2873 (Pubitemid 21916521)
11. M.S. Co, N.M. Avdalovic, P.C. Caron, M.V. Avdalovic, D.A. Scheinberg, and C. Queen Chimeric and humanized antibodies with specificity for the CD33 antigen J. Immunol. 148 1992 1149 1154
12. S.A. Marshall, G.A. Lazar, A.J. Chirino, and J.R. Desjarlais Rational design and engineering of therapeutic proteins Drug Discov. Today 8 2003 212 221 (Pubitemid 36298676)
13. D.J. Mandell, and T. Kortemme Computer-aided design of functional protein interactions Nat. Chem. Biol. 5 2009 797 807
14. H. Fazelinia, P.C. Cirino, and C.D. Maranas Extending iterative protein redesign and optimization (IPRO) in protein library design for ligand specificity Biophys. J. 92 2007 2120 2130 (Pubitemid 46495273)
15. M. Berrondo, J.J. Gray, and R. Schleif Computational predictions of the mutant behavior of AraC J. Mol. Biol. 398 2010 462 470
16. S.W. Chi, C.Y. Maeng, S.J. Kim, M.S. Oh, C.J. Ryu, S.J. Kim, K.H. Han, H.J. Hong, and S.E. Ryu Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism Proc. Natl. Acad. Sci. U.S.A. 104 2007 9230 9235
17. G.A. Jeffrey An Introduction to Hydrogen Bonding 1997 Oxford University Press Oxford
18. D.A. Case, T.E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K.M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, and R.J. Woods The Amber biomolecular simulation programs J. Comput. Chem. 26 2005 1668 1688 (Pubitemid 43076180)
19. W.D. Cornell, P. Cieplak, C.I. Bayley, R. Gould, K.M. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J. Caldwell, and P.A. Kollman A second-generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 1995 5179 5197
20. W. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, and M. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
21. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
22. J.P. Ryckaert, G. Ciccotti, and H.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
23. W. Jiang, M. Hodoscek, and B. Roux Computation of absolute hydration and binding free energy perturbation distributed replica-exchange molecular dynamics J. Chem. Theory Comput. 5 2009 2583 2588
24. H.J. Böhm The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J. Comput.-Aided Mol. Design 8 1994 243 256