We describe a novel method to calculate the packing interactions in protein structural models. The method calculates the interatomic occluded surface areas for each atom in the protein model. The identification of, and degree of interaction with, neighboring atoms is accomplished by extending surface normals from a dot surface of each atom to the point of intersection with neighboring atoms. The combined occluded and non-occluded surface areas may be normalized for the amino acid composition of the protein providing a single parameter, the normalized protein surface ratio, which is diagnostic for native-like structures. Individual residues in the model which are in infrequent occluded surface environments may be identified. The method provides a means to explicitly describe packing densities and packing environments of individual atoms in a protein model. Finally, the method allows estimation of the complementarity between any interacting molecules, for example a ligand binding to a receptor.
The (110) faces of lysozyme crystals in their mother liquor have been investigated using an atomic force microscope (AFM) in height mode. Crystal growth and dissolution steps, as well as simultaneous growth and dissolution in pits, have been observed. Screw dislocations were also observed but the fine structure has not yet been investigated. Images that may possess molecular resolution were obtained and compared with theoretical images based on the crystallographic structure and the effects of arbitrary tip profiles. Crystallographic periodicities of 38 and 112 A were observed. A recurring feature is a centered periodic array of minima that may be associated with one of the two nearly planar sheets of molecules present in the crystal that are parallel to the (110) faces.
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