Computer modeling of actinomycin D interactions with double-helical DNA

We have performed molecular mechanical calculations on intercalation complexes of actinomycin D with a series of base-paired hexanucleoside pentaphosphates; d(GCGCGC)2, d(GCCGGC)2, d(GCATGC)2, d(GCTAGC)2 and d(ATGCAT)2. Our results are in good agreement with previous experimental work on sequence selectivity. The results provide a rationalization for the strong preference of actinomycin D to intercalate on the 3' side of guanine residues, consistent with previously proposed models. Finally, the computed structures for d(ATGCAT)2-actinomycin D complexes have been compared with two-dimensional nuclear magnetic resonance nuclear Overhauser effect experimental results. To our knowledge, this is the first extensive comparison of molecular mechanical model structures for a drug-DNA complex with experimental solution phase data. We find generally good agreement between our computational models and the experimental solution phase structures.     

Energetics of protein structure and folding

The available experimental date on the kinetics of unfolding and refolding of small proteins are reviewed. Excluding slow transitions in the unfolded protein due to cis–trans isomerization of peptide bonds, the rate-limiting transition state in both unfolding and refolding is concluded to be a high-energy distortion of the fully folded state. Partially folded intermediates are undoubtedly important for folding, but their formation is normally not rate limiting. A simple model is used to illustrate some of the aspects of protein-folding energetics.     

Calcium domains associated with individual channels can account for anomalous voltage relations of CA-dependent responses.

Computer-assisted modeling of calcium influx through voltage-activated membrane channels predicted that buffer-limited elevation of cytoplasmic free calcium ion concentration occurs within microscopic hemispherical "domains" centered upon the active Ca channels. With increasing depolarization, the number of activated channels, and hence the number of Ca domains, should increase; the single-channel current should, however, decrease, thereby decreasing Ca2+ accumulation in each domain relative to the macroscopic current. Such voltage dependence of the microscopic distribution of Ca2+ may influence relations between total Ca2+ entry and Ca-dependent processes. Ca-mediated inactivation of Ca channels in Aplysia neurons exhibits behavior consistent with the calcium domain hypothesis.     

Circular dichroism spectroscopy of the intermediates that precede the rate-limiting step of the refolding pathway of bovine pancreatic trypsin inhibitor. Relationship of conformation and the refolding pathway

Circular dichroism spectra of the partially folded trapped intermediates were measured in order to aid in the elucidation of the conformational forces which determine a nonrandom, nonsequential pathway of disulfide bond formation upon refolding of bovine pancreatic trypsin inhibitor. Whatever conformation was responsible for the kinetic rates of the intermediates should be stabilized by the presence of their trapped disulfide bonds. The near-ultraviolet spectra provide considerable information about the environments of the aromatic and disulfide side chains. The predominant single-disulfide intermediate has significant nonrandom conformation not present in the fully reduced protein, with aromatic rings and the disulfide bond in stabilized asymmetric environments. Forming either of the two nonnative, but kinetically important, second disulfides in this intermediate does not produce unequivocably different conformations. Forming a second native, but kinetically unproductive, disulfide produces a substantial decrease in randomness, which may hinder formation of the third disulfide. The largest conformational changes occur upon disulfide rearrangement to the stable, correctly refolded, two- and three-disulfide species. Interpretation of the far-ultraviolet spectra in terms of the secondary structure of the intermediates is uncertain, due to the atypical spectra of the folded forms of the protein. Consequently, we are unable to determine unambiguously the secondary structure of the intermediates. However, all the spectra show that nonrandom conformations of the polypeptide chain gradually appear as disulfide bond formation progresses, as expected from the nonrandom pathway of the latter.     

Comparison of the tryptophan synthetase alpha-subunits of several species of Enterobacteriaceae

Creighton, T. E. (Stanford University, Stanford), D. R. Helinski, R. L. Somerville, and C. Yanofsky. Comparison of the tryptophan synthetase alpha subunits of several species of Enterobacteriaceae. J. Bacteriol. 91:1819-1826. 1966.-The tryptophan synthetase alpha subunits of Escherichia coli K-12, E. coli B, Shigella dysenteriae, Salmonella typhimurium, and Aerobacter aerogenes have been purified and their structures compared. Each of these alpha subunits exhibits a sedimentation coefficient of about 2.7S. Peptide patterns of trypsin plus chymotrypsin digests of the alpha subunits have indicated that all of the alpha subunits have peptide regions in common. The patterns of E. coli K-12, E. coli B, and S. dysenteriae alpha subunits appear to be nearly identical, whereas the alpha subunits from S. typhimurium and A. aerogenes differ from those of E. coli and from each other. It has also been shown that the E. coli structural gene for the alpha subunit is translated identically in E. coli and S. typhimurium.     

A clarification of two congeners,Pseudodiaptomus lobipes and P. binghami (Calanoida,Pseudodiaptomidae) from India,with description of P. mixtus sp.n. from Bangladesh

Two closely related and often confused species of Pseudodiaptomus from the Lobus-species group, P. lobipes and P. binghami are redescribed from various locations along the east coast of India. These species predominately occur in freshwater though they can survive temporary periods of increased salinity. The distinctive features of the species are found on: female caudal ramal setae, female and male urosome 1–2 spinulation patterns, and fifth legs. A new species P. mixtus from Bangladesh is described.     

Amphetamine Promotes Neostriatal Ascorbate Release via a Nigro-Thalamo-Cortico-Neostriatal Loop

Abstract: In the neostriatum, amphetamine and other dopamine agonists elevate the extracellular level of ascorbate, which is known to modulate neostriatal function. Although both D₁ and D₂ receptors have been linked to neostriatal ascorbate release, ample evidence suggests it is controlled by areas outside the neostriatum. The present series of experiments used selective lesions and intracerebral drug infusions to probe the involvement of the ventromedial thalamus and substantia nigra pars reticulata. Our results implicate both of these sites in amphetamine-induced increases in the release of neostriatal ascorbate. Thus, whereas unilateral electrolytic lesions of the substantia nigra pars reticulata completely abolished the ability of systemic amphetamine (2.5 mg/kg) to increase extracellular ascorbate in ipsilateral neostriatum, intranigral infusions of this drug (10 and 30 µg/µl) elevated neostriatal ascorbate release. This infusion effect, moreover, was blocked by electrolytic lesions of the ipsilateral ventromedial thalamus, which receives input from the substantia nigra pars reticulata and projects to the cerebral cortex. These results, combined with previous evidence implicating cortical projections to neostriatum as the source of extracellular ascorbate, suggest that neostriatal ascorbate release is regulated, at least in part, by a nigro-thalamo-cortico-neostriatal pathway.