ANTIBODY MODELING

Relevent publications

• Pellequer, J.-L., Chen, S.-w. W., Bell, C. W., Feeney, A., Karu, A. E., Li, K., Li, Q. X., and Roberts, V. A., (2000) "Architecture of Antibody Binding Sites for Polynuclear Aromatic Hydrocarbons", American Chemical Society Symposium Series, in press.
• Pellequer, J.-L., Zhao, B., Kao, H.-I., Bell, C. W., Li, K., Li, Q. X., Karu, A. E., and Roberts, V. A., (2000) "Stabilization of Bound Polycyclic Aromatic Hydrocarbons by a pi-Cation Interaction ", J. Mol. Biol., 302, 691-699.
• Smithrud, D. B., Benkovic, P. A., Benkovic, S. J., Roberts, V. A., Liu, J., Iwama, S., Phillips, B. W., Neagu, I., Smith, A. B., III, Hirschmann, R., (2000) "Cyclic Peptide Formation Catalyzed by an Antibody Ligase", Proc. Natl. Acad. Sci, USA, 97, 1953-1958.
• Pellequer, J.-L., Chen, S. W., Roberts, V. A., Tainer, J. A., and Getzoff, E. D., (1999) "Unravelling the Effect of Changes in Conformation and Compactness at the Antibody VL-VH Interface Upon Antigen Binding", J. Mol. Recog., 12, 267--275.
• Thayer, M. M., Olender, E. H., Arvai, A. S., Koike, C. K., Canestrelli, I. L., Stewart, J. D., Benkovic, S. J., Getzoff, E. D., and Roberts, V. A., (1999) "Structural Basis for Amide Hydrolysis Catalyzed by the 43C9 Antibody", J. Mol. Biol., 291, 329--345.
• Wiens, G. D., Roberts, V. A., Whitcomb, E. A., O'Hare, T. O., Stenzel-Poore, M. P., and Rittenberg, M. B., (1998) "Harmful Somatic Mutations: Lessons From the Dark Side", Immunol. Rev., 162, 197-209.
• Brown, M., Rittenberg, M. B., Chen, C., and Roberts, V. A., (1996) "Tolerance to Single, but Not Multiple, Amino Acid Replacements in Antibody V_H CDR2: A Means of Minimizing B Cell Wastage from Somatic Hypermutation", J. Immunol., 156, 3285-3291.
• Pulito, V. L., Roberts, V. A., Adair, J. R., Rothermel, A. L., Collins, A. M., Varga, S. S., Martocello, C., Bodmer, M., Jolliffe, L. K., and Zivin, R. A., (1996) "Humanization and Molecular Modeling of the Anti-CD4 Monoclonal Antibody, OKT4A", J. Immunol., 156, 2840-2850.
• Roberts, V. A. and Getzoff, E. D., (1995) "Metalloantibody Design", FASEB J., 9, 94-100.
• Chen, C., Roberts, V. A., Stevens, S., Brown, M., Stenzel-Poore, M. P., and Rittenberg, M. B., (1995) "Enhancement and Destruction of Antibody Function by Somatic Mutation: Unequal Occurrence is Controlled by V Gene Combinatorial Associations", EMBO J., 14, 2784-2794.
• Bell, C. W., Roberts, V. A., Scholthof, K.-B. G., Zhang, G., and Karu, A. E., (1995) "Recombinant Antibodies to Diuron: A Model for the Phenylurea Combining Site", in Immunoanalysis of Agrochemicals, Emerging Technologies, Nelson, J. O., Karu, A. E., and Wong, R. B., eds., American Chemical Society, Washington D. C., 50-71.
• Roberts, V. A., Stewart, J. D., Benkovic, S. J., and Getzoff, E. D., (1994) "Catalytic Antibody Model and Mutagenesis Implicate Arginine in Transition-State Stabilization", J. Mol. Biol., 235, 1098-1116.
• Chen, C., Roberts, V. A., and Rittenberg, M. B., (1992), "Generation and Analysis of Random Point Mutations in an Antibody CDR2 Sequence: Many Mutated Antibodies Lose Their Ability to Bind Antigen", J. Exp. Med., 176, 855-866.
• Roberts, V. A., Iverson, B. L., Iverson, S. A., Benkovic, S. J., Lerner, R. A., Getzoff, E. D., and Tainer, J. A., (1990), "Antibody Remodeling: A General Solution to the Design of a Metal-Coordination Site in an Antibody Binding Pocket", Proc. Natl. Acad. Sci. USA, 87, 6654-6658.
• Chien, N. C., Roberts, V. A., Giusti, A. M., Scharff, M. D., and Getzoff, E. D., (1989), "Significant Structural and Functional Change of an Antigen Binding Site by a Distant Amino Acid Substitution: Proposal of a Structural Mechanism," Proc. Natl. Acad. Sci. USA, 86, 5532-5536.