COMPUTER MODELING OF PROTEIN AND PEPTIDE STRUCTURE AND MOLECULAR INTERACTIONS

Victoria A. Roberts, Ph.D.

Assistant Professor, Department of Molecular Biology

Page designed by Angela L. Walker

V. A. Roberts, E. H. Olender, J. L. Pellequer, M. E. Pique, M. M. Thayer, S. J. Benkovic1, A. E. Karu2, R. J. Nachman3, L .F. Ten Eyck4.
1The Pennsylvania State University, University Park, PA
2University of California, Berkeley, CA
3U.S. Department of Agriculture, College Station, TX
4San Diego Supercomputer Center, San Diego, CA

Key words: antibodies, catalytic antibodies, computer modeling, molecular dynamics, molecular interactions, molecular modeling, peptide conformation, protein design.

Visit some of our collaborators at TSRI: [E. D. Getzoff] [J. A. Tainer]

The rapid increase in the number of known protein sequences and structures is fueling the need to develop methods for predicting protein structure and intermolecular interactions. We use computational and computer graphics techniques in conjunction with site-directed mutagenesis, peptide synthesis, and protein crystallography to develop testable hypotheses and direct protein engineering.

Our database of superimposed crystallographic antibody structures reveals the structural conservation of both the antibody backbone fold and the side chains that shape the antigen-binding pocket. With the database, we constructed a three-dimensional model of the antibody 43C9, which efficiently catalyzes the hydrolysis of specific amides and esters. From the model, two amino-acid side chains were identified as being key for catalysis and two metal-binding mutants were designed. These hypotheses were verified by site-directed mutagenesis, but neither metal-binding mutant displayed catalytic activity. In collaboration with E. Getzoff, crystallographic structures are being determined to define the placement and geometry of the metal-binding sites. Although one loop making up part of the antigen-binding site has a different conformation in the crystallographic structure than in the model, the rest of the structure is quite similar, including placement of the two catalytic side chains. In another project, models were built for two antibodies that bind polyaromatic hydrocarbons, which are significant environmental contaminants. The antigen-binding sites have two positively charged side chains (Fig. 1), which may enhance the binding specificity of the antibodies.

  • PREDICTING MACROMOLECULAR COMPLEXES

     The computer program DOT has been developed to predict intermolecular interactions. DOT performs a complete, six-degree-of-freedom search of all configurations between two molecules. The search algorithm is very fast and is not directly dependent on the size of the molecules being investigated, allowing it to be applied to proteins. DOT is currently being tested on two types of systems: electron-transport proteins, which represent transient protein/protein interactions, and the DNA-repair enzyme uracil-DNA glycosylase (UDG), which forms an irreversible complex with an inhibitor, the protein UGI (Fig. 2). Results from DOT are being verified by comparison with the crystallographic structures of the complexes.

  • ACTIVE CONFORMATIONS OF INSECT NEUROPEPTIDES

     Neuropeptides control diverse functions in living organisms. Surprisingly, neuropeptides found in insects often have sequence similarity to mammalian neuropeptides, suggesting the existence of neuropeptide superfamilies with shared conformational determinants. Conformational preferences determined by molecular dynamics simulations combined with structure/activity studies have led to the design of constrained cyclic analogs, highly active simplified linear analogs, and the first nonpeptidal ligand for an insect neuropeptide/receptor system.

    Figure legends

    Fig. 1. Computational model of an anti-benzo(a)pyrene antibody. The model reveals a deep pocket into which a benzopyrene molecule (center, dark tubes) fits snuggly. On the left side of the binding pocket is a lysine side chain and on the right side is an arginine side chain (black tubes extending from white Ca backbone), both of which may contribute to binding through cation-p interactions.

    Fig. 2. The most favorable interactions between UDG and UGI found by DOT surround the position of UGI in the crystallographic structure of the UDG/UGI complex. A slicing plane through the three-dimensional field of intermolecular interaction energies determined by DOT is colored from most favorable (white) to least favorable (dark). White tubes (center) represent the Ca backbone structure of UDG visible above the plane. The black sphere represents the center of UGI in the crystallographic complex. The dark region surrounding UDG is the area that the center of UGI cannot enter because of steric clashes between the two molecules.

  • PUBLICATIONS

     Nachman, R.J., Roberts, V.A., Lange, A.B., Orchard, I., Holman, G.M., Teal, P.E.A. Active conformation and mimetic analog development for the pyrokinin--PBAN--diapause--pupariation and myosuppressin insect neuropeptide families. In: Phytochemicals for Pest Control. Hedin, P.A., Hollingworth, R.M., Masler, E.P., Miyamoto, J., Thompson, D.G. (Eds.). American Chemical Society, Washington DC, 1997, p. 277.

    Roberts, V.A., Nachman, R.J., Coast, G.M., Hariharan, M., Chung, J.S., Holman, G.M., Williams, H., and Tainer, J.A. Consensus chemistry and b-turn conformation of the active core of the myotropic/diuretic insect neuropeptide family. Chem. and Biol. 4:105, 1997.