Principal torsion angles of collective motions in biomolecules: A study of a single base opening in DNA duplexes

Large amplitude collective motions in biomolecules primarily involve the displacement of a number of torsion angles of rotatable bonds. This work tests the hypothesis that one or a few of these angles are the principal variables that act as the reaction coordinate for a particular motion. Our study on a low energy single base opening in DNA duplexes identified one such coordinate. This torsion angle together with the accompanying geometric requirement on other angles have been used to determine the pathway of the opening process. The energetics along the pathway has also been analyzed based on widely used molecular mechanics force field parameters. Our results support the proposed hypothesis and further tests on other collective motions in different systems are warranted.