Preliminary Analysis of Water Molecule Distributions in Proteins

Abstract

In order to check the validity of force fields used in simulation studies it is necessary to have sufficient experimental structural data available with which to compare the simulated results. Accumulation of a large enough quantity of structural data is especially important for interactions for which the stereochemical constraints are expected to be fairly weak such as in the biologically important application of modelling the aqueous environment of proteins. We present a preliminary analysis of such experimental structural data for water molecules around the main chain and some sidechain atoms from 16 high resolution proteins. In general the distribution of water molecules around polar groups are fairly broad. However, where distinct preferential geometries are seen, they agree well with the expected stereochemistry and iso-energy contour maps. The broader distributions are shown to be due to the effects of a water molecule making multicontacts to the protein surface which may be characteristic of a specific secondary structure or sequence.

Key Words:

• Proteins
• aqueous environments
• polar graphs