College Park, Maryland      June 6 - 10 , 2004

MP11: A Method to Predict Small-angle Neutron Scattering Intensities of Nucleic Acids from High-resolution Structures

J. Zhou (Department. of Chemistry, UMBC, Baltimore, MD), S. Krueger (NIST Center for Neutron Research), S Gregurick (Department of Chemistry, UMBC, Baltimore, MD)

Based on the original program, Xtal2sas, which calculates model SANS intensities of proteins from high-resolution structures, we propose a method to obtain model SANS intensities from nucleic acids. For a high-resolution structure of a nucleic acid, either from x-ray crystallography or structural prediction, we generate an ellipsoidal cylinder model for each nucleotide with calculated radii, length and volume from the coordinates file, e. g.: a PDB file. Each ellipsoidal cylinder is filled with random points of the appropriate neutron scattering length density using a Monte Carlo method, and is superimposed on each nucleotide to represent the overall structure of the nucleic acid. The distance distribution function, P(r) is calculated by summing all possible pairs of points in the structure. Then, the scattering intensity I(Q) is then calculated through a Fourier transform of P(r). We extend the original program, Xtal2sas, for both proteins and nucleic acids, and we test our approach on a few examples of nucleic acids to check the effectiveness of this method.

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