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

• Published in: Biophysical journal 2000, Vol.78 (1), p.70-78
• Main Authors: Banachowicz, Ewa, Gapiński, Jacek, Patkowski, Adam
• Format: Article
• Language: English
• Subjects: Biology; DNA - chemistry; Models, Molecular; Nucleic Acid Conformation; Oligodeoxyribonucleotides - chemistry; Physics; Polymers; Protein Conformation; Proteins - chemistry; RNA - chemistry; Software; Solutions
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/S0006-3495(00)76573-8

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 σ = 5.0 Å was chosen on the basis of a comparison of the calculated translational diffusion coefficients ( D T) and the rotational relaxation times ( τ R) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D T and τ R of tRNA Phe. Better agreement with the experimental data was achieved for slightly larger σ = 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 D T of small proteins were used to establish the optimum value of σ = 4.5 Å for amino acids. The lack of experimental data on τ R for proteins restricted the tests to the translational diffusion properties.