WATER

How does water contribute to the structure and behaviour of biological molecules?

How does water contribute to the structure and behaviour of biological molecules?

Introduction

The structure of liquid water and its interaction with biological molecules is a very active area of experimental and theoretical research. The chemically complex surfaces of protein molecules alter the structure of the surrounding layer of hydrating water molecules. The dynamics of hydration water can be detected by a series of experimental techniques, which show that hydration waters typically have slower correlation times than water in bulk. Specific water-mediated interactions in protein complexes have been studied in detail, and these interactions have been incorporated into potential energy functions for protein folding and design (Klare, 2001, 89).

The subtle changes in the structure of hydration water have been investigated by theoretical studies. Water is the medium in which all life occurs. Biological molecules are bathed in it, and the interactions of proteins, nucleic acids and membranes with water shape their structures and functions. Water has well-known bulk properties that are governed by the small size, dipole moment, polarizability and hydrogen bonding ability of individual water molecules.

Water molecules make very intimate interactions with biological macromolecules, and hydration shell waters have properties that differ significantly from bulk. The effects of interactions with surfaces typically do not extend far into the water, usually only one to two hydration shells. Furthermore, water molecules interact differently with polar and nonpolar groups. Polar groups favor direct interactions with water molecules, whereas nonpolar groups enhance interactions among the water molecules themselves.

As biological molecules nearly always have heterogeneous surface chemistry, the interactions of biological surfaces with interfacial water are complex. In this review, I will focus primarily on recent experimental and theoretical studies of water interactions with protein molecules. Water interactions with nucleic acids and membranes have been reviewed elsewhere. Recent work on water structure and interfaces ranges from measurements of the structural details of bulk water to analysis of the distributions of localized water molecules in the interior of proteins and at protein-protein interfaces. Experimental techniques are being used to measure the hydration of proteins and probe the time scales of hydration processes at protein, membrane and nucleic acid surfaces. The effects of water interactions are being incorporated into potential energy functions for protein folding, structure prediction and design

How many hydrogen bonds does water make?

It can be argued that the single most interesting property of water is its ability to form hydrogen bonds. This cohesive property, combined with its geometry, results in the many unusual properties of water. Xu and Dill have used a very simple 2D water model consisted of a fixed geometry with hydrogen bonds to recover the temperature dependence of the hydrophobic effect. By contrast, other research groups have increased the complexity of their water models by moving from classical fixed-charge models to those that include polarizability, flexibility and quantum effects.

One example is the AMOEBA force field that includes polarization and accurately reproduces experimental and ab initio simulation ...