Normal mode analysis of a nucleic acid with flexible furanose rings in dihedral angle space

Abstract

Normal mode analysis in dihedral angle space is performed for a nucleic acid. In the analysis, the conformational change of a flexible sugar ring, so-called pseudo-rotational motion, is treated by a pseudo-rotation variable. This treatment in dihedral angle space allows the rings to be either flexible or rigid. Comparison of normal mode analyses with and without the pseudo-rotational motions has revealed a significant influence of the flexibility of the sugar rings on the static and dynamic conformation of nucleic acids. Assumed rigidity of sugar rings leads to a significant deviation of the minimum energy conformation and disappearance of some collective motions which are necessary to account for a high fraction of atomic fluctuations. Normal mode analysis in Cartesian coordinate space is also performed for the same nucleic acid. It is found that modes with frequencies below 20 cm−1 have 80% of the contribution of the total mean-square atomic fluctuation and are represented dominantly by motions caused by dihedral angles and pseudo-rotations only. This indicates that low-frequency modes from both analyses in dihedral angle space and in Cartesian coordinate space span the same subspace. Consequently, normal mode analysis in dihedral angle space, including pseudo-rotation variables, can be applied to nucleic acids in order to determine and characterize their dynamics.