Richard S. Morgan

A new method for computing the macromolecular electric potential

A general methodology is developed for the rigorous computation of the electrostatic potential for a protein of arbitrary shape, assuming the presence of linear dielectric media. The theory proceeds by considering the distribution of induced polarization charge at the dielectric interface, rather than by attempting a direct solution of Poissons equation (as in the finite-difference approach of Warwicker & Watson). The method is applied to a study of two-dimensional model proteins, where it is shown that the presence of a cleft is associated with a region of relatively high potential in the solvent medium. The results of a preliminary calculation in three dimensions for the protein lysozyme are also discussed; again, a region of enhanced potential is observed near the cleft at the active site. Our computational evidence supports the suggestion of Warwicker & Watson that clefts are associated with important electrostatic effects.

A survey of amino acid side-chain interactions in 21 proteins.

Abstract Based on the atomic co-ordinate data for 21 representative proteins, the frequencies of long-range interactions between side-chain groups and 15 different types of side-chain atoms have been determined. The observed frequencies are compared to the results expected for random association in order to define a scale of relative affinities. Thirty-five residue-atom pairs exhibit frequencies of interaction that differ by at least 50% from the expected values. The amino acids tend to fall into three classes: non-polar, neutral and polar amino acids. The data are regrouped in a different way to determine the average affinity of each amino acid side-chain group for all other types of side-chain groups. Fourteen side-chain pairs have at least 50% fewer interactions than expected, while 21 side-chain pairs have at least 50% more interactions than expected. Unusual patterns of association are discussed and compared with current ideas about the organization of protein structure.

A survey of atomic interactions in 21 proteins.

All of the long-range atomic interactions in 21 representative proteins of known tertiary structure have been categorized by atom types, considering 15 different types of side-chain atoms and four different types of backbone atoms. The observed distribution of atomic interactions is compared to the distribution expected for random interactions in order to detect specific interaction tendencies. Nine types of interactions yield observed values that differ by more than 50% from the expected values. 1. (a) Sulfur atoms are attracted to other sulfur atoms and avoid negatively charged oxygen (O−) atoms. 2. (b) (O−) atoms tend to interact with NH3+, >NH, OH and polar CH2 groups. 3. (c) Carbonyl oxygen atoms frequently associate with neutral and polar CH2 groups. 4. (d) Carbonyl carbon atoms are often found near NH3+ atoms. The various atom types are ranked in terms of a scale of affinities based on the types of atoms most frequently found in their environment.

The symmetry of self-complementary surfaces

Abstract The concept of molecular complementarity is defined, and a theorem given which describes the symmetry required of self-complementary surfaces. We show in detail that the surfaces of chymotrypsin and concanavalin A have this symmetry, while that of the α chain of human deoxyhemoglobin does not.

Structure of ribosomes of chromatoid bodies - Three-dimensional Fourier synthesis at low resolution.

A three-dimensional Fourier synthesis at an axial resolution of 75 angstroms of optical diffraction data from electron micrographs of stained sections of chromatoid bodies reveals the position of the large and small ribosomal subunits within these crystals of ribosomes.

Zinc in Entamoeba invadens

Atomic absorption spectroscopy, electron microprobe analysis, and dithizone staining of trophozoites and cysts of Entamoeba invadens demonstrate that these cells have a high concentration of zinc (approximately 10-6 microgram per cell or 1 percent of their dry weight). In the cysts of this organism, the zinc is confined to the chromatoid bodies, which previous work has shown to contain crystals of ribosomes. The chemical state and function of this zinc are unknown.

Tryptophan content and fluorescence of cysts of Entamoeba invadens

Abstract Evidence is presented that cysts of Entamoeba invadens contain large amounts (approximately 4 · 10−5 μg) of a chemical entity whose ultraviolet absorption, fluorescence, oxidation and reaction with p-dimethyl-aminobenzaldehyde closely parallels that of a rare amino acid, tryptophan. Since previous work has shown that this entity lies within the cysts Chromatoid Bodies (which contain ribosomes in regularly packed, helical arrays), the conclusion is reached that Chromatoid Bodies are cocrystals of tryptophan (in some form) and ribosomes.