Dynamics of conformation change

Biological macromolecules often undergo changes in shape carrying out their biological function. For example the action of muscle fibers involves a relative rotation of a section of a macromolecule. An important change in shape in DNA is the B to A conformation change that is caused by changes in the level of hydration of the helix. The A conformation is the low hydration form. In that transition no valence bonds, and likely no H-bonds, are even transiently disrupted. The change is mostly to the helicity of the helix, going from a complete turn in 10 base pairs to one in 11 base pairs. In the process the width of the helix increases, the length decreases, and the base pairs tilt away from the perpendicular to the helix axis (Saenger, 1984). Analysis of this transition has been carried out in the context of a soft mode displacive change transition (Eyster and Prohofsky, 1977; Lindsay et al., 1985). Displacive change is useful for transitions that involve continuous movement of atoms from one conformation to another, i.e. where the transition is second order. The mode that goes soft, in soft mode analysis, is related to the softening of the free energy barrier that separates the free energy minima as a function of order parameter, as discussed in a previous chapter.