Refinement of human lysozyme at 1.5 Å resolution analysis of non-bonded and hydrogen-bond interactions

The structure of human lysozyme has been crystallographically refined at 1.5 Å resolution by difference map and restrained least-squares procedures to an R factor of 0.187. A comprehensive analysis of the non-bonded and hydrogen-bonded contacts in the lysozyme molecule, which were not restrained, revealed by the refinement has been carried out. The non-bonded CC contacts begin at ~3.45 Å, and the shorter contacts are dominated, as expected, by interactions between trigonal and tetrahedral carbon atoms. The CO contact distances have a “foot” at 3.05 Å. The CN distance plot shows a significant peak at 3.25 Å, which results from close contact between peptide NHs and carbonyl carbons involved in N_iC′_{i ? 2} interactions in α-helices and reverse turns. The distances involving sulphur atoms discriminate SC trigonal interactions at 3.4 to 3.6 Å from SC tetrahedral interactions at 3.7 Å. All these types of non-bonded interactions show minimum distances close to standard van der Waals' separations.Analysis of hydrogen-bond distances has been carried out by using standard geometry to place hydrogen atoms and measuring the XHO distances. On this basis, there are 130 intramolecular hydrogens: 111 NHO bonds, of which 69 are between main-chain atoms, 13 between side-chain atoms and 29 between mainchain and side-chain atoms. If a cluster of four well-defined internal water molecules is included in the protein structure, there is a total of 19 OHO hydrogen bonds. The mean NO, NHO distances and HN?O angles are 2.96 ± 0.17 Å, 2.05 ± 0.18 Å and 18.5 ± 9.6 °, and the mean OO, OHO distances and HÔO angles are 2.83 ± 0.19 Å, 1.98 ± 0.26 Å and 23.8 ± 13.4 °. The distances agree well with standard values, although the hydrogen bonds are consistently more non-linear than in equivalent small molecules. An analysis of the hydrogen-bond angles at the receptor atom indicates that the α-helix, β-sheet and reverse turn have characteristic angular values. A detailed analysis of the regularity of the α-helices and reverse turns shows small but consistent differences between the α-helices in lysozyme and the current standard model, which may now need revision. Of the 21 reverse turns that include a hydrogen bond, the conformations of 19 agree very closely with four of the five standard types. We conclude that the restrained least-squares method of refinement has been validated by these analyses.     

Axonal Transport of the Ca2+-Dependent Protein Modulator of 3'':5''-Cyclic-AMP Phosphodiesterase in the Rabbit Visual System

Water-soluble proteins were extracted from individual retinas, optic nerves, combined optic tracts and lateral geniculate bodies, and superior colliculi of rabbits at 1, 3, and 18 days after injection of [3H]leucine into the right eye. The Ca2+-dependent protein modulator of 3':5'-cyclic-AMP phosphodiesterase (calmodulin) was isolated from these samples by a two-step polyacrylamide gel electrophoresis procedure. An analysis of the radioactivity incorporated into the total soluble proteins and the calmodulin revealed that most of the calmodulin was axonally transported at a slow rate (2--4 mm/day) and represented about 0.45% of the total transported soluble protein.     

A.C. cable theory and its implications on the measurements of the membrane electric parameters

The solution to the a.c. cable equations for a leaky non-inductive coaxial cable is presented. It is shown that the exact solution can be expressed in terms of a simple Ohm's law formulation modified by multiplicative factors. A numerical analysis of these factors shows that the formulation reduces to a simple Ohm's law for the case of infinite impedance terminations, if the voltage is recorded at a distance 0·421/λ from the centre of a midpoint current injection, 1 is the half-length of the cell and A the space constant. The same result applies to the case of external current injection if the voltage is recorded at a distance of 0·581/λ from the centre of the cell segment of length 21. This thus allows an easy and accurate computation of the membrane resistance and capacitance. It is also shown that the accuracy obtained in these computations can be estimated quantitatively. The actual values of the accuracy obtained in a.c. studies of Nitella translucens are presented.     

Modification of cell membrane in variants of chinese hamster cells resistant to abrin

Stable and heritable variants of Chinese hamster ovary (CHO) cells which are resistant to different levels (0.1, 1.0 and 10 μg/ml) of the toxin abrin have been isolated and characterized. The frequency of resistant colonies to abrin was increased with the concentration of a chemical mutagen. There was no effect of cell density or cross-feeding on the recovery of variants. In experiments using fluorescein-labeled abrin and ricin which bind to terminal (non-sialylated) galactose residues of cell-surface oligosaccharides, parental cells exhibited strong binding toward both toxins, whereas no fluorescence was observed in the resistant clones. A fluorescein-conjugated lectin, BS II, which is specific for terminal N-acetyl- -glucosaminyl residues, did not interact with the parental cells, but did with the resistant clones. This suggests that on the surface of resistant cells the number of terminal galactosyl residues of oligosaccharide chains in glycoproteins was reduced, exposing the penultimate N-acetyl- -glucosaminyl residues. The number of available endogenous acceptor sites for galactosyl transferase in the abrin-resistant clones was directly proportional to the degree of resistance. In the presence of great excess of exogenous acceptor, the rates of galactosyl transfer were similar in all the abrin-resistant cell types tested, with levels ranging from 1.4 to 1.7 times parental cell values. Studies with tetraploid cell hybrids reveal that resistance was a recessive trait. Fluctuation analysis showed that abrin resistance occurred in CHO cell populations at a rate of 4−7 × 10⁻⁸/cell/generation. The system may serve as a new marker for quantitative mutagenesis studies.     

Spectral analysis of high resolution direct-derivative melting curves of DNA for instantaneous and total base composition.

Derivative melting profiles of DNA have been obtained directly by recording the difference in absorbance between two identical solutions maintained at a small constant temperature differential. This deltaA is monitored continuously with increasing temperature in a ratio recording spectrophotometer. Resolution of complex hyperfine structure in the profiles of small homogeneous viral DNAs appears to be significantly better than has been produced by various numerical methods of differentiation. In addition, a spectral method has been modified that permits easy analysis for DNA base composition from the ratio of derivative melting curves obtained at 282 and 260 nm. Eight bacterial and three vertebrate DNAs have been analyzed for total base composition from the product of the instantaneous base composition at small temperature intervals (0.05 degrees C) throughout the entire melting region and the integrated area of the 282 nm profile. The results are in excellent agreement with values determined by traditional methods.     

Evaluation of fasciotomy and vasodilator for treatment of frostbite in the dog

Severe freezing injury was produced in the hind foot of 26 mongrel dogs. All dogs were given daily whirlpool treatment and protective bandaging for 14 days following injury. In addition, certain dogs received a vasodilator, fasciotomy, or both vasodilator and fasciotomy following injury. Deep foot temperatures, foot volumes, tissue pressures, and 14 day tissue loss-salvage scores were compared. Significant differences between fasciotomy and nonfasciotomy dogs were seen in foot temperature, volume, and tissue pressure immediately following fasciotomy. Though there was no significant difference in 14 day tissue loss, there was clinically apparent prolongation of integrity of the local vascular system for 2 to 5 days following fasciotomy, and total foot salvage in several dogs receiving fasciotomy.     

A Search for the Intermediate Radical, ONOO', in the Reaction Between Oxygen and Nitric Oxide in Solution

The most probable initial reaction between NO and O₂ is direct addition to give the peroxyl radical ONOO. In view of the potential importance of this radical in biology, we have searched extensively for its formation, using EPR spectroscopy and rapid freezing techniques. At best, only extremely low concentrations were detected, and in most systems, no signals were detectable. We conclude that this radical is unlikely to be of major importance per se in biological systems, in contrast with its one electron adduct, the peroxynitrite anion.     

Bioalkylation of dibenz[a,b]anthracene in rat liver cytosol

Previous studies by other investigators have established that L-region methyl derivatives of dibenz[a,h]anthracene (DBA) were more carcinogenic than the parent hydrocarbon. The bioalkylation of DBA was investigated by incubating the hydrocarbon with rat liver cytosol fortified with S-adenosyl-L-methionine (SAM) in 0.1 M phosphate buffer (pH 7.4) for 1 h at 37 degrees C in air. The reaction was stopped by the addition of cold acetone and the mixture extracted with ethyl acetate and washed with water. The organic phase was evaporated and the residue dissolved in methylene chloride for analysis by reverse phase high performance liquid chromatography (HPLC) and gas chromatography/mass spectroscopy GC/MS. Products were found that were indistinguishable from 7-methyl-DBA and 7,14-dimethyl-DBA, 7-hydroxymethyl-DBA, 7-hydroxymethyl-14-methyl-DBA, and 7,14-dihydroxymethyl-DBA. The results suggest that unsubstituted carcinogenic hydrocarbons are preprocarcinogens that react with SAM in liver cytosol preparations, to form alkyl substituted procarcinogens, which are more potent than the corresponding preprocarcinogens.