X-ray studies of water in crystals of lysozyme

• Published in: Journal of molecular biology Vol. 167; no. 3; pp. 693 - 723
• Main Authors: Blake, C.C.F., Pulford, W.C.A., Artymiuk, P.J., Huber, R.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 05.07.1983
• Subjects: albumen; Animals; Binding Sites; Humans; Hydrogen Bonding; lysozyme; man; Muramidase; Protein Conformation; Testudo; Turtles; Water; X-ray crystallography; X-Ray Diffraction
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(83)80105-3

The structure of the water in crystals of human and tortoise egg-white lysozyme, which contain about 350 and about 650 water molecules per protein molecule, respectively, has been studied by X-ray refinement at high resolution. In the crystals, 60 to 80% of the total water is represented by featureless electron density filling the crystal interstices, which can be modelled to a first approximation by a single-valued, smoothed electron density continuum. The number of ordered water molecules detected is 140 for human and 128 for tortoise. These ordered water molecules are either hydrogen-bonded to protein polar groups, or hydrogen-bonded to other bound water molecules, to form a single layer around the protein molecules. Estimates of the proportion of the protein surface covered by ordered water molecules have been obtained by contact area calculations, giving a lower limit of ∼45%, an upper limit of ∼85% and a “best” estimate of ∼75%. Examination of the structure of the ordered water layer shows that it is probably not any other single regular structure, and suggests that there is a local ordering controlled by the nature of the protein surface. Nearly all exposed protein polar atoms interact with ordered water molecules with, on average, protein oxygen atoms interacting with twice as many water molecules as protein nitrogen atoms. Analysis of the relation of the B-factors of the bound water molecules to the B-factors of the protein atoms to which they are bound, suggests that the 33 to 35 water molecules that make multiple hydrogen bonds with the lysozyme molecules are strongly bound, and that the 95 to 105 waters that make single hydrogen bonds to the protein or other bound water molecules are more weakly bound. Comparison of the location of the bound water molecules in the two lysozymes shows that most of the multiply bound water molecules occupy similar binding sites, suggesting that crystal packing or the presence of salt ions does not have a dominating influence on the protein-water interaction, which therefore may correspond to that in solution.