3 - Dynamics of proteins, nucleic acids, and their solvent surroundings

Summary

In this chapter, we provide an overview of the dynamics of water, aqueous solutions, proteins and nucleic acids. Our intent is to provide some sense of the relationships among the different types of motion that will be separately examined in later chapters. We also review a number of basic concepts that will be used extensively in what follows. As with the preceding chapter, this general discussion is not complete. Additional details will be introduced where appropriate in other chapters.

Water and aqueous solutions

At a temperature of 300 K, liquid water has enough kinetic energy that a typical pair of hydrogen bonded molecules will separate and form new bonds with other neighbors in a time of roughly 4ps. Smaller displacements of the molecules, corresponding to deformations or transient breaks in hydrogen bonds, occur on a shorter time scale. As a result of this underlying molecular mobility, bulk water behaves as a moderately viscous fluid except at times below about 0.1 ps, where the rigidity of the hydrogen bonded structure becomes apparent.

Solute molecules influence the molecular motion of water in a variety of ways. As described in the preceding chapter, the structure of liquid water adjacent to small hydrophobic solutes is similar to that of bulk water. The mobility of water in hydrophobic hydration shells is slightly reduced in comparison to bulk water, in part because of the reduced number of hydrogen bonding rearrangements available to a water molecule adjacent to the solute.