Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins

Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed alpha-helix on a right-twisted antiparallel or parallel beta-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the alpha-helix to the beta-sheet. The packing was investigated for a CH3CO-(L-Ala)16-NHCH3 alpha-helix interacting with five-stranded beta-sheets composed of CH3CO-(L-Val)6-NHCH3 chains. All internal and external variables for both the alpha-helix and the beta-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the alpha-helix interacting with both the parallel and the anti-parallel beta-sheet. The classes differ in the orientation of the axis of the alpha-helix relative to the direction of the strands of the right-twisted beta-sheet. In the class with the most favorable arrangement, the alpha-helix is oriented along the strands of the beta-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the alpha-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the beta-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted beta-sheet. In the other, it is oriented along the concave diagonal of the beta-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel beta-sheet are generally similar, although the antiparallel beta-sheet has been found to be more flexible. The major features of 163 observed alpha/beta packing arrangements in 37 proteins are accounted for in terms of the computed structural preferences. The energetically most favored packing arrangement is similar to the right-handed beta alpha beta crossover structure that is observed in proteins; thus, the preference for this connectivity arises in large measure from this energetically favorable interaction.     

Purine nucleoside synthesis, an efficient method employing nucleoside phosphorylases

An improved method for the enzymatic synthesis of purine nucleosides is described. Pyrimidine nucleosides were used as pentosyl donors and two phosphorylases were used as catalysts. One of the enzymes, either uridine phosphorylase (Urd Pase) or thymidine phosphorylase (dThd Pase), catalyzed the phosphorolysis of the pentosyl donor. The other enzyme, purine nucleoside phosphorylase (PN Pase), catalyzed the synthesis of the product nucleoside by utilizing the pentose 1-phosphate ester generated from the phosphorolysis of the pyrimidine nucleoside. Urd Pase, dThd Pase, and PN Pase were separated from each other in extracts of Escherichia coli by titration with calcium phosphate gel. Each enzyme was further purified by ion-exchange chromatography. Factors that affect the stability of these catalysts were studied. The pH optima for the stability of Urd Pase, dThd Pase, and PN Pase were 7.6, 6.5, and 7.4, respectively. The order of relative heat stability was Urd Pase greater than PN Pase greater than dThd Pase. The stability of each enzyme increased with increasing enzyme concentration. This dependence was strongest with dThd Pase and weakest with Urd Pase. Of the substrates tested, the most potent stabilizers of Urd Pase, dThd Pase, and PN Pase were uridine, 2'-deoxyribose 1-phosphate, and ribose 1-phosphate, respectively. Some general guidelines for optimization of yields are given. In a model reaction, optimal product formation was obtained at low phosphate concentrations. As examples of the efficiency of the method, the 2'-deoxyribonucleoside of 6-(dimethylamino)purine and the ribonucleoside of 2-amino-6-chloropurine were prepared in yields of 81 and 76%, respectively.     

Study of the mitotic and meiotic chromosomes of sotol (<i>Dasylirion cedrosanum</i> Trel.)

The genus Dasylirion is a group of plants typically present in the Chihuahuan Desert, perennial, with a dioecious sexual behavior and commonly called sotoles. This genus has been little studied from the biological point of view, and the bases of its reproductive response remain unknown. In this work we studied the chromosome number and meiotic response of Dasylirion cedrosanum in the county of Saltillo, Coahuila, located at the North East of Mexico. For the preparation of mitotic chromosomes, we used a technique based on enzymatic treatment with pectolyase and cellulase, as well as staining with acetocarmin dye. For the study of meiosis, male flower buds were collected, fixed and stained for analysis with the same dye. As a result, the gametic (n = x = 19) and somatic chromosome (2n = 38) numbers of D. cedrosanum are reported for the first time, being consistent with previous findings in other Dasylirion species, which points to a constant ploidy level across the genus. Variation was observed in the morphology and size of the somatic chromosomes, with types ranging from submetacentric to subtelocentric, and sizes oscillating in a range of 4.43 µm, with an average total length of 112.38 µm for the diploid chromosome complement. This shows that the chromosome complement of D. cedrosanom would belong to a 3B classification of Stebins, with a medium variation between chromosome lengths and low chromosome asymmetry. This variation indicates the feasibility of constructing a chromosome ideotype for this species. The meiotic chromosome pairing showed a chromosome behavior consistent with a disomic inheritance characteristic of a diploid species, with prevalence of ring and chain bivalents, typically without pairing abnormalities. Bivalent configurations in all cases were symmetrical.The normal and symmetrical meiotic pairing indicates a balanced production of gametes, and suggests the absence of heteromorphic sex determination.     

Primate origins and evolution. By R. D. Martin. Princeton,NJ: Princeton University Press. 1990. ISBN 0-691-08565-X. xiv + 840 pp. $125 (cloth)

Dental emergence ages are examined for a mixed longitudinal sample of 58 chimpanzees of known age and sex (22 males, 36 females) followed over the past 10 years. This study provides the most complete data set currently available on dental emergence in chimpanzees of known age and sex. Summary statistics and cumulative frequency percentiles of emergence ages are presented for both the permanent and the primary teeth. Male and female percentiles are also compared and reveal a number of cases of sexual dimorphism in emergence ages. Comparisons of emergence means reveal some statistically significant differences between upper and lower teeth but not between antimeres in the upper or lower dentition. Kendall's rank correlation coefficient (tau) suggests a correlation in timing between first molar and incisor emergence within individuals. In addition, a significant time lag was observed between first molar and central incisor emergence. A number of emergence sequence polymorphisms are presented as well. These findings provide important baseline information for future studies of chimpanzee growth, development, and demography and also contribute to several current issues in paleoanthropology relating to dental maturation patterns in early hominids.     

Radiation response of cells during altered protein thiol redox

The major focus of this work was to investigate how altered protein thiol redox homeostasis affects radiation-induced cell death. We used the cells of wild-type CHO cell line K1, the CHO cell line E89, which is null for G6PD activity, and a radiation-sensitive CHO cell line, XRS5. The protein-thiol redox status of cells was altered with cell-permeable disulfides, hydroxyethyldisulfide (HEDS) or lipoate. HEDS is primarily reduced by thioltransferase (glutaredoxin), with GSH as the electron donor. In contrast, lipoate is reduced by thioredoxin reductase. HEDS was reduced at a greater rate than lipoate by G6PD-containing K1 (wild-type) cells. Reduction of disulfides by G6PD-deficient cells was significantly slower with HEDS as substrate and was nearly absent with lipoate. The rate of reduction of HEDS by E89 cells decelerated to near zero by 30 min, whereas the reduction continued at nearly the same rate during the entire measurement period for K1 cells. HEDS treatment decreased the GSH and protein thiol (PSH) content more in G6PD-deficient cells than in G6PD-containing cells. On the other hand, lipoate did not significantly alter the protein thiol, but it increased the GSH in K1 cells. Acute depletion of GSH by l-buthionine-sulfoximine (l-BSO) in combination with dimethylfumarate significantly decreased the rate of reduction of HEDS by K1 cells close to that of G6PD-deficient cells. Prior GSH depletion by l-BSO alone significantly decreased the PSH in glucose-depleted E89 cells exposed to HEDS, but this did not occur with K1 cells. The radiation response of G6PD-deficient cells was significantly sensitized by HEDS, but HEDS did not have this effect on K1 cells. The DNA repair-deficient XRS5 CHO cells displayed the same capacity as K1 cells for HEDS reduction, and like K1 cells the XRS5 cells were not sensitized to radiation by HEDS treatment. Deprivation of glucose, which provides the substrate for G6PD in the oxidative pentose phosphate cycle, decreased the rate of bioreduction of HEDS and lipoate in G6PD-containing cells to the level in G6PD-deficient cells. In the absence of glucose, HEDS treatment diminished non-protein thiol and protein thiol to the same level as those in G6PD-deficient cells and sensitized the K1 cells to HEDS treatment. However, depletion of glucose did not alter the sensitivity of XRS5 cells in either the presence or absence of HEDS. Overall the results suggest a major role for pentose cycle control of protein redox state coupled to the activities of the thioltransferase and thioredoxin systems. The results also show that protein thiol status is a critical factor in cell survival after irradiation.     

Impaired collateral development in mature rats

The effect of maturation on collateral development of resistance arteries was investigated. Three to four sequential mesenteric arteries were ligated to create collateral pathways in anesthetized young (approximately 200 g) and mature (approximately 600 g) rats. Blood flow was similarly elevated in collaterals of young and mature animals. In vivo inner arterial diameter was increased only within young collaterals (33 +/- 7%, P < 0.001). Increases in number of intimal nuclei (57 +/- 10% vs. 52 +/- 14%) and cross-sectional medial area (33 +/- 13% vs. 38 +/- 5%) were similar between young and mature collaterals. Relative to the same animal controls, collateral endothelial nitric oxide synthase mRNA was increased as much in mature as in young rats. Proteomic analysis revealed significant differences in protein expression with maturation between control arteries as well as flow-loaded collateral vessels. The results indicate that, whereas intimal and medial remodeling events were similar in collaterals of young and mature rats, luminal expansion occurred only in young rats. Alteration in arterial protein expression with maturation and altered responses to stimuli for collateral development may contribute to this impairment.     

G6PD deficient cells and the bioreduction of disulfides: effects of DHEA, GSH depletion and phenylarsine oxide

We used Glucose 6 phosphate dehydrogenase (G6PD) minus cells (89 cells) and G6PD containing cells (K1) to understand the mechanisms of bioreduction of disulfide and the redox regulation of protein and non protein thiols in mammalian cells. The 89 cells reduce hydroxyethyldisulfide (HEDS) to mercaptoethanol (ME) at a slower rate than K1 cells. HEDS reduction results in loss of nonprotein thiols (NPSH) and a decrease in protein thiols (PSH) in 89 cells. The effects are less dramatic with K1 cells. However, the loss of NPSH and PSH in K1 cells are increased in the absence of glucose. Glutathione-depletion with L-BSO partially blocks HEDS reduction in K1 and 89 cells. Treatment with the vicinal thiol reagent phenyl arsenic oxide (PAO) blocks reduction of HEDS in both cells. Surprisingly, dehydroepiandrosterone (DHEA), a known inhibitor of G6PD, inhibits the growth and blocks the reduction of HEDS both in 89 and K1 cells suggesting that its mechanism for inhibition of growth is not G6PD related.