SUNY at Albany
June 19-23, 2001
Modelling Large-Scale Structural Dynamics of DNA Macromolecule
The new methodology of the adequate model construction is proposed for the description of the large-scale dynamics of the DNA double helix. Using the four-mass model approach developed earlier (1-3) for the investigation of the low-frequency vibrations of the double helix and taking into account the peculiarities of the macromolecule structure, the possibility of the modelling of such important DNA transformations as conformational transition and melting is demonstrated.
For the description of the large-scale motions in the DNA double helix the generalized four-mass model is presented. The model takes into consideration (first) the motions of the nucleotides as a single whole with respect to its positions in the helical strand, (second) the motions of the nucleosides with the respect to the backbone chain and (third) intranucleoside mobility. The force field of the model is formed by the base interactions in the hydrogen bonded pairs, conformational rearrangement energy of the sugar rings, base stacking and backbone structural elements interactions along the chain. The interaction of the bases with water molecules is taken into account under investigation of the opening process in DNA. The model parameters and the potential functions view are determined for the description of the conformational rearrangements on the definite pathways of double helix motion (4,5).
By going to the consideration of the joint motions of the DNA structural elements the model may be reduced to the two-component form. One component is the degree of freedom of the elastic rod and another - the internal coordinate of the conformational transformation. It is shown that the kinetic energy for all considered structural transformations of the such heterogeneous macromolecule as DNA may be put in the homogeneous form.
On the basis of the proposed approach the results of the large-scale dynamics study for DNA macromolecule are discussed. The conclusion is made about the existence of the two types of DNA conformational mobility: sensitive and insensitive to macromolecule heterogeneity.
References and Footnotes
Bogolyubov Institute for Theoretical Physics, National Academy of Science of Ukraine, Kiev, Ukraine 03143 email: firstname.lastname@example.org; Fax: 380 (44) 266-5998; Phone: 380 (44) 266-9159