Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

Water plays an essential role in most biological processes. Water molecules solvating biomolecules are generally in fast exchange with the environment. Nevertheless, well-defined electron density is seen for water associated with proteins whose crystal structure is determined to high resolution. The relative accessibility of these water sites is likely to be relevant to their biological role but is difficult to assess. A time-averaging crystallographic refinement simulation on basic pancreatic trypsin inhibitor successfully characterizes the relative accessibility of the crystallographic water sites. In such a refinement simulation water diffuses through the crystal lattice in a manner that is consistent with the crystallographic data. This refinement discovers that internal crystallographic waters in this particular protein are bridged to the outside protein surface via a series of progressively more accessible water sites. On the surface of the protein, water molecules exchange quickly between crystallographic water sites. Time-averaging crystallographic refinement provides a view based on experimental data of the relative accessibility of water sites in and around a protein in a crystalline environment. Proteins 1999;36:501-511.