Introduction

The biological importance of large scale intramolecular motions is obvious. Such motions are an essential part of protein folding, the binding of ligands by proteins, and allosteric effects in enzymes. They are important in a variety of interactions between macromolecules, including the aggregation of antibodies (Yguerabide, Epstein & Stryer, 1970; Hanson, Yguerabide & Schumaker, 1985), the formation of the protein coat of viruses (Harrison, 1978), muscle contraction (Huxley, 1969; Harrington, 1971; Harvey & Cheung, 1982; Eisenberg & Hill, 1985), and the packaging of DNA in the nucleosome (Olins & Olins, 1974; Kornberg, 1974; Levitt, 1978; Sussman & Trifonov, 1978). They may be coupled to local intramolecular motions of the kind described in chapter 6, for example in the repuckering of sugars accompanying the transitions between the A, B and Z conformations in DNA, or in the formation of the environments necessary for some local structural transitions.

Motions that involve most or all of the atoms in a macromolecule occur over a wide range of time scales. The fastest of these motions are small amplitude vibrations whose characteristic times in the absence of solvent (determined from normal mode calculations) may range up to 10 ps. When the effects of solvent are included, the time scale can increase substantially, because the motions are no longer free, undamped oscillations. The time scale will depend on such factors as the masses of the molecular fragments, the elastic force opposing the motion, the friction due to the solvent, and the relative magnitudes of the inertial and viscous forces in the solvent dynamics (the Reynolds number).