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Biophys J, January 2000, p. 70-78, Vol. 78, No. 1

Solution Structure of Biopolymers: A New Method of Constructing a Bead Model

Ewa Banachowicz, Jacek Gapinski, and Adam Patkowski

Molecular Biophysics Laboratory, Institute of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland

We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius sigma  = 5.0 Å was chosen on the basis of a comparison of the calculated translational diffusion coefficients (DT) and the rotational relaxation times (tau R) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation DT and tau R of tRNAPhe. Better agreement with the experimental data was achieved for slightly larger sigma  = 5.7 Å. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of DT of small proteins were used to establish the optimum value of sigma  = 4.5 Å for amino acids. The lack of experimental data on tau R for proteins restricted the tests to the translational diffusion properties.

Biophys J, January 2000, p. 70-78, Vol. 78, No. 1
© 2000 by the Biophysical Society   0006-3495/00/01/70/09  $2.00


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