Refinement of the F-actin model against X-ray fiber diffraction data by the use of a directed mutation algorithm.
The F-actin model has been refined by a Directed Mutation Algorithm, a reiterative procedure which combines a Monte-Carlo method of selecting subdomains to be refined at each cycle with a non-linear least-squares routine to get the best fit for the particular selected domains. The G-actin crystal structure was used as a starting model. The experimental data were obtained by X-ray fiber diffraction patterns from oriented F-actin gels. After 250 cycles we were able to obtain an almost perfect fit of the calculated diffraction pattern to the experimental diffraction pattern as well as a reasonable stereochemistry including intermolecular interactions of the actin monomers with an r.m.s. shift in the C alpha-positions of 3.2 A from the crystal coordinates. The stereochemistry of the intersubunit packing was calculated by molecular dynamics using the program X-PLOR. In addition, the binding site of phalloidin, a cyclic heptapeptide from the mushroom Amanita phalloides, could be determined. Furthermore, we were able to determine differences in the structures of F-actin with and without phalloidin. The method proved itself robust and showed a high degree of convergence.
Lorenz
M
M
Max-Planck Institut für medizinische Forschung Abetilung Biophysik, Heidelberg.
Popp
D
D
Holmes
K C
KC
D000199:Actins / Q000737:chemistry*; D000465:Algorithms; D000595:Amino Acid Sequence; D008433:Mathematics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D016297:Mutagenesis, Site-Directed; D010590:Phalloidine; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry; D014961:X-Ray Diffraction / Q000379:methods
D000199:Actins; D011994:Recombinant Proteins; D010590:Phalloidine