X-ray studies of water in crystals of lysozyme. 1983

C C Blake, and W C Pulford, and P J Artymiuk

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 approximately 45%, an upper limit of approximately 85% and a "best" estimate of approximately 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.

UI MeSH Term Description Entries
D009113 Muramidase A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17. Lysozyme,Leftose,N-Acetylmuramide Glycanhydrolase,Glycanhydrolase, N-Acetylmuramide,N Acetylmuramide Glycanhydrolase
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D006860 Hydrogen Bonding A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds. Hydrogen Bonds,Bond, Hydrogen,Hydrogen Bond
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D014426 Turtles Any reptile including tortoises, fresh water, and marine species of the order Testudines with a body encased in a bony or cartilaginous shell consisting of a top (carapace) and a bottom (plastron) derived from the ribs. Sea Turtles,Terrapins,Tortoises,Sea Turtle,Terrapin,Tortoise,Turtle,Turtle, Sea,Turtles, Sea
D014867 Water A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Hydrogen Oxide
D014961 X-Ray Diffraction The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Xray Diffraction,Diffraction, X-Ray,Diffraction, Xray,Diffractions, X-Ray,Diffractions, Xray,X Ray Diffraction,X-Ray Diffractions,Xray Diffractions

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