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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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We evaluate an empirical potential energy function and associated parameters for classical molecular dynamics simulations of lecithins, a common class of lipid. The physical accuracy of the force field was tested through its application to molecular dynamics simulations of the known crystal structures of lipid molecules. Average atomic positions and molecular conformation are well maintained during the simulations despite considerable thermal motion. Calculated isotropic temperature factors correlate highly with those from experiment.

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X-ray diffraction studies have produced a low resolution image and also located the iron atoms of a monomeric hemerythrin from muscles of a sipunculan worm. These results reveal the course of the polypeptide chain and some details of the active center.Oxygen transport in certain invertebrate animals is mediated by hemerythrin in erythrocytes of the coelomic fluid. Hemerythrin usually occurs as an octamer of 108,000 molecular weight. It is a non-heme iron protein containing two iron atoms per subunit and it reversibly binds oxygen in the ratio 1 02:2 Fe. Much study has been attended to the structural chemistry of this evolutionary alternative to hemoglobin as an oxygen carrier (1), particularly by Klotz and coworkers, but many details remain obscure. New light can now be shed on hemerythrin structure following the discovery by Klippenstein et al. (2) that the sipunculan worm Themiste (syn. Dendrostomum) pyroides (3) contains a monomeric hemerythrin in its retractor muscles as well as hemerythrin octamers in its erythrocytes-a situation reminiscent of myoglobin and hemoglobin in mammals. Several properties of this myohemerythrin suggest that it bears close structural similarity to the protomers of octameric hemerythrin (2, 4).Myohemerythrin from T. pyroides has been crystallized (4) and the first structural results from studies of these crystals are reported here. These results are mainly at low resolution, but owing to a high helix content and recourse to chemical data, more molecular detail has been gleaned than is ordinarily discernible at low resolution. By way of warning it should be noted that published interpretations of low-resolution density maps have sometimes later been proved incorrect. However, it seems unlikely that such mistakes are repeated here. The quality of this map and the consistency of the model with independent chemical data argue for the basic correctness of the rather detailed molecular interpretation given here.Myohemerythrin is a relatively small protein of 118 aminoacid residues and molecular weight 13,900. This facilitates its crystallographic analysis. In turn, the knowledge of this structure should simplify the analysis of octameric hemerythrins. In any event, further studies on myohemerythrin should be an avenue for gaining a detailed understanding of reversible oxygenation in this fascinating class of proteins. X-ray analysCrystals of metazide myohemerythrin were grown as previously described (4) and then transferred to a stabilizing medium of 80% saturated ammonium sulfate buffered to pH 6.7. These crystals are in space group P2,2121 and have unit cell dimensions of a = 41.58 A; b = 80.03 A; and c = 37.78 X. Derivatives were prepared by soaking native crystals in stabilizing media containing heavy-atom compounds.Many compounds seem to bind, but derivative crystals are often prone to cracking and poor isomorphism. Nevertheless, five derivatives were found to be good enough at least for lowresolution phasing.X-ray diffraction data were measured by w-scans on a fourcircle di...