STRUCTURE MODEL OF A COMPLEX BETWEEN THE FACTOR FOR INVERSION STIMULATION (FIS) AND DNA - MODELING PROTEIN-DNA COMPLEXES WITH DYAD SYMMETRYAND KNOWN PROTEIN STRUCTURES

A method is presented to predict overall conformations of protein-DNA complexes on the basis of the known three-dimensional structures of th e proteins. The method is restricted to proteins with a common twofold symmetry axis, which show only minor conformational changes upon bind ing to DNA. The method uses a numerical finite difference solution of the linearized Poisson-Boltzmann equation and subsequent energy minimi zation cycles. Structural parameters-the rotation angle of the DNA rel ative to the protein around the common symmetry axis, the protein-DNA distance, and intermolecular hydrogen-bonding contacts-are presented f or two test cases, DNA bound to CAP (catabolite gene activator protein ) and to the Cro-repressor of bacteriophage 434. The DNA curvature in the starting model of the docking procedure was chosen as a smoothed a pproximation of the conformation found in the X-ray structures of thes e complexes. The method is further used to predict the unknown structu re of the complex between the factor for inversion stimulation (FIS) a nd DNA, which is bent upon binding to FIS. In contrast to the test cas es, the unknown curvature of the starting model is derived from a cali bration of electrostatic precalculations for different proteins accord ing to crystallographically observed DNA bending. The results of the m odeling are in good accordance with the experimentally observed overal l structure of protein-DNA complexes for the two test cases; for FIS, they correspond to several of the experimentally proposed protein-DNA contacts. (C) 1996 Wiley-Liss, Inc.