Thermodynamic cycle-perturbation study of the binding of trifluoroacetyl dipeptide anilide inhibitors with porcine pancreatic elastase

The variety of results of crystallographic studies of the serine proteases complexed with isocoumarin inhibitors presents a challenging problem to modeling methods and molecular energetics. Therefore, the thermodynamic cycle-perturbation technique has been used to study a model system of elastase and two peptidic inhibitors. Using the program AMBER, the technique correctly predicts changes of the binding constants for the trifluoroacetyl dipeptide inhibitors in comparison with available experimental (kinetic and crystallographic) data. However, the absolute values obtained are shown to be sensitive to the specific electrostatic interaction potential parameters used in the simulations. The reader and user are cautioned that thermodynamic cycle-perturbation results may be too optimistic by underestimating the accuracy of free energy values. This is especially a matter of concern for those cases where a direct comparison with experimental values is not possible, viz., (1) the stimulation of binding of novel compounds, (2) structurally uncertain binding sites, or (3) structurally different binding modes. With our best 4-31G* ESP (electrostatic potential) charges we were able to reproduce experimentally determined free energy differences (delta delta A) with an accuracy of about 1.5 kcal/mol. Dynamically induced structural changes in the binding site of elastase, and particularly changes in hydrogen-bond patterns of the binding site, are also reported.     

The induction of chromosomal damage in rat hepatocytes and lymphocytes II. Alkylation damage and repair of rat-liver DNA after diethylnitrosamine,dimethylnitrosamine and ethyl methanesulphonate in relation to clastogenic effects

Rat-liver DNA alkylation by diethylnitrosamine (DEN), dimethylnitrosamine (DMN) and ethyl methanesulphonate (EMS) was studied in an attempt to relate chromosome-damaging effects of these agents (the formation of micronuclei in hepatocytes; see preceding paper) to specific alkylation patterns. No correlation was observed between the induction of micronuclei and liver DNA N-alkylation, measured as 3- and 7-alkyl-purines. O⁶-Alkylguanine is probably not involved in micronucleus induction because it is lost from DNA too rapidly to explain the much more persistent clastogenic effects. In contrast, both the initial amounts of alkylphosphotriesters and the persistencies of these products roughly paralleled the respective effects on micronucleus induction. The possible involvement of alkylphosphotriesters or other O-alkylation products of comparable stabilities is discussed. Results with DMN suggest that part of the primary DNA methylation damage is converted into a secondary (DNA) lesion and that both the primary and secondary lesion(s) contribute to the process of micronucleus formation.     

The expression, purification and crystallization of the epsilon subunit of the F1 portion of the ATPase of Escherichia coli.

The epsilon subunit of the F0F1-ATPase from Escherichia coli has been expressed in E. coli as a fusion protein with glutathione S-transferase from the parasitic helminth Schistosoma japonicum. The epsilon subunit released by thrombin treatment of the purified fusion protein carried two amino acid changes, A1G and M2S, and was obtained in a yield of about five milligrams per litre of cultured cells. The two amino acid changes were shown not to affect function. The protein has been crystallized in a form suitable for X-ray diffraction structure analysis. The crystals are hexagonal, space group P6(1)22 (or P6(5)22), with a = b = 94.9 A, c = 57.1 A and gamma = 120 degrees. The diffraction from small crystals extends to at least 2.9 A resolution.     

Variable mutagenic activity of commercial preparations of ABTS (2,2'-azino-di(3-ethyl-benz-thiazoline) sulphonic acid

Different batches of ABTS obtained from the same commercial source varied in their capacity to effect direct mutation in the strains of Salmonella typhimurium used routinely in the incorporation test of Ames. One batch, obtained in 1976, and another obtained early in 1979, both exhibited direct base-pair substitution and frame-shift activities. These activities, however, were absent from each of two batches obtained after 1979, and also from a highly purified preparation from a different source. The possible presence of the unsulphonated immediate precursor of ABTS as a mutagenic impurity is an unlikely explanation for the activity of the mutagenic preparations. It is more probable that the commercial synthesis generated other, mutagenic, impurities which remained in the batches obtained in 1976 and early in 1979, but were absent or were removed from later batches. The identity of these active impurities is unknown. Pure ABTS is neither a direct nor an indirect mutagen.     

Segments of Djungarian hamster chromosomes, specific for translocation of integration of amplified mdr1 genes, do not possess increased instability]

Earlier we have revealed in Djungarian hamster DM-15 cells three chromosomal segments (2p22, 5p1, 7q23-25) that are specific for transposition of amplified mdr1 genes from the site of location of resident gene copy (it was mapped to 4q21-23). In situ hybridization revealed in wild type cells no mdr1 homologous sequences in all these three segments. In this work we studied distribution of chromosomal breakages induced in DM-15 cells by aphidicolin, 5-fluorodeoxyuridine or N-phosphonacetyl-L-aspartate. The data obtained indicate that two of above mentioned segments. 2p22 and 7q23-25, contain no fragile sites. So, specificity of these segments for the transposition of amplified mdr1 genes is not due to their particular instability or to the presence in them of sequences homologous to amplifiable selectable gene.