Poster Sessions

SB -1

Yaroslav Ryabov

Y. Ryabov, C. Schwieters

Structure determination of protein-protein complexes using parameters of their overall rotational dynamics available via NMR relaxation data.

Structure and dynamics of proteins have obvious mutual relationships. For example, the size and shape of a protein determine rates of its overall rotational tumbling. Recently, a fast method for calculation of protein diffusion tensors has become available. This method is 500 times faster than conventional bead algorithms. We report the implementation of this fast method within the Xplor-NIH structure determination package. We utilize the overall protein shape restraints encoded in components of protein diffusion tensor for positioning and orienting domains in protein complexes. We illustrate application of this method for the particular case of the HIV-1 protease homodimer. In this case the first 5 percent of the sorted list of refined structures contain structures which are practically equivalent to each other (0.001 angstrom of Ca rmsd) and very close to the reference NOE based HIV-1 structure (0.3 angstrom of Ca rmsd). The average value of energy function for these structures with lowest rmsd is about 5 times lower than this for the structure immediately following them in the list. This proves the ability of the method to obtain correct arrangement of protein’s subunits for the cases when reference structure is not available a priori.