Topological mirror images in protein structure computation: an underestimated problem.

When calculating three-dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.     

Studies on the interactions of glycerol dehydrogenase from Bacillus stearothermophilus with Zn2+ ions and NADH

The interactions of the essential divalent cation, Zn2+, with the binary complex formed between glycerol dehydrogenase (glycerol:NAD+ 2-oxidoreductase, EC 1.1.1.6) and its coenzyme NADH have been examined by fluorescence spectroscopy. Both the metallo and non-metallo form of the enzyme bind the coenzyme NADH. The addition of Zn2+ ions to a solution of the binary complex formed between metal-depleted enzyme and NADH results in a rapid increase in fluorescence emission at 430 nm. This has been used to determine the on rate for Zn2+ to the enzyme/binary complex. A dissociation constant of 3.02 +/- 0.25.10(-9) M for the equilibrium between Zn2+ ions and the enzyme has been determined.     

The rapid purification of 3-hydroxybutyrate dehydrogenase and malate dehydrogenase on triazine dye affinity matrices.

3-Hydroxybutyrate dehydrogenase (EC 1.1.1.30) and malate dehydrogenase (EC 1.1.1.37) were purified to homogeneity on a large scale involving only two sequential affinity-chromatography steps on two triazine dye-Sepharose matrices. Recoveries of both enzymes were in excess of 60%. Malate dehydrogenase could also be purified by a combination of triazine dye affinity chromatography and gel filtration on Ultrogel AcA-44, but this offered no significant advantage over the purely affinity procedure.     

Captopril in renovascular hypertension: long-term use in predicting surgical outcome.

The angiotensin converting-enzyme inhibitor captopril was used as long-term preoperative treatment in a series of hypertensive patients with unilateral renal arterial disease. There were immediate and sustained falls in plasma angiotensin II and aldosterone concentrations, with converse increases in circulating renin and angiotensin I. In patients with sodium and potassium deficiency and secondary aldosterone excess before treatment captopril corrected the sodium and potassium deficits; in these cases the initial hypotensive response was profound but the later effect was less pronounced. When sodium and potassium state was initially normal it remained unchanged during captopril treatment, while the full hypotensive effect took up to three weeks to be attained. The immediate, but not long-term, falls in arterial pressure with captopril were proportional to the immediate decrements of plasma angiotensin II. Nevertheless, while the immediate blood-pressure reduction with captopril variously overestimated and underestimated the eventual surgical response, the absolute blood-pressure values during long-term captopril related well with those after operation. Pretreatment plasma renin and angiotensin II concentrations, while closely predicting the immediate captopril response, are fallible guides to surgical prognosis. In contrast, long-term treatment with converting-enzyme inhibitors may provide an accurate indication of surgical outcome.     

The effect of lactation length on the circulating concentrations of progesterone and oestradiol in the early weaned sow

Eighteen crossbred multiparous sows were allocated at random to one of two lactation lengths: 42 or 10 days. All sows were mated at the oestrus after weaning and from mating until day 26 post coitum they were bled every second day. Progesterone and oestradiol concentration in the plasma was determined by radioimmunoassay. Progesterone increased more rapidly between days 4 and 10 post coitum in early weaned sows and the oestradiol surge at mating was abnormally extended for the same group.     

Effect of diffusion limitations and floc size distributions on fermentor performance and the interpretation of experimental data

The biological rate equation that describes the overall rate of substrate uptake by microbial films has been extended to microbial flocs with the aid of a shape parameter. The “solid”- and liquid-phase diffusion limitations are explored and found to depend largely on a dimensionles characteristic size k₂¹V_p/A_p. Procedures are discussed by which k₂¹V_p/A_p can be determined from experimental data on the conversion efficiency in a completely mixed fermentor and measurements carried out on flocs recovered from the fermentor are assessed. Floc size distributions are shown to affect the performance characteristics of a fermentor when some of the flocs are sufficiently large to exhibit a diffusional limitation, and it is concluded that a single mean floc size (k₂¹V_p/A_p)* is sufficient to characterize a given distribution, at least when all the flocs are geometrically similar. The mean floc size closely corresponds to the “surface” mean floc size of the floc size distributions.     

Activation of Phycomyces adenosine 3', 5'-monophosphate phosphodiesterase by blue light.

Cyclic AMP phosphodiesterase can be extracted from sporangiophores of $\text{Phycomyces}\text{blakesleeanus}$. Activity is enhanced by 1–10 μM FAD and FMN but not by riboflavin. Moderate intensity of blue light also activates the enzyme, especially in the presence of 1mM GTP. The enzyme must be extracted and stored in the absence of blue light for this result. Forty times the intensity of red light has no effect. This finding is consistent with the very sudden transient drop in cyclic AMP level upon light stimulation in the intact sporangiophore.     

Affinity chromatography on immobilised nucleotides. Some applications to the purification of thermophilic dehydrogenases and kinases.

The effect of pH and temperature on the capacity and binding of Bacillus stearothermophilus, alcohol dehydrogenase and phosphofructokinase to N6-(6-aminohexyl)-5'-AMP-Sepharose has been examined. Specific elution from the substituted AMP-Sepharose was examined using a variety of cofactors, fragments of cofactors and substrates. A purification scheme for each enzyme on the substituted AMP-Sepharose using nucleotides and gradients of pH and salt is presented. Interestingly, elevated temperature increased the affinity of both enzymes for N6-(6-aminohexyl)-5'-AMP-Sepharose, however, the Michaelis constant for nucleotide determined at various temperatures remained constant. The effect of pH and salt concentration on the binding of B. stearothermophilus glyceraldehyde-3-phosphate dehydrogenase to 6-aminohexanoyl-NAD+-Sepharose was also examined; raising the pH above 7.5 lowers the capacity of the matrix and the effect of a range of ammonium sulphate concentrations on the adsorption of the enzyme was examined. A specific purification of glyceraldehyde-3-phosphate dehydrogenase from partially purified extracts of this organism was achieved.     

Role of carbohydrate in determining the immunochemical properties of the major glycoprotein (gp71) of Friend murine leukemia virus.

Treatment of Friend leukemia virus gp71 with protease-free glycosidase enzymes results in removal of the major portion of the carbohydrate without affecting the amount of protein present. The digested material migrates as protein of about 60,000 to 65,000 molecular weight on sodium dodecyl sulfatepolyacrylamide gel electrophoresis. Analyses of the serological properties of gp71 after enzyme treatment indicated that the type, group, and interspecies determinants were not destroyed. In contrast, treatment with proteolytic enzymes led to the complete destruction of the gp71 molecule, including the total elimination of its serological reactivity as measured by direct and competition radioimmunoassay and by a serum cytotoxicity assay. We conclude that the carbohydrate portion of gp71 is not of major significance in defining the antigenic determinants of this viral glycoprotein.