Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides

Helical parameters displayed on a Ramachandran plot allow peptide structures with successive residues having identical main chain conformations to be studied. We investigate repeating dipeptide main chain conformations and present Ramachandran plots encompassing the range of possible structures. Repeating dipeptides fall into the categories: rings, ribbons, and helices. Partial rings occur in the form of “nests” and “catgrips”; many nests are bridged by an oxygen atom hydrogen bonding to the main chain NH groups of alternate residues, an interaction optimized by the ring structure of the nest. A novel recurring feature is identified that we name unpleated β, often situated at the ends of a β‐sheet strand. Some are partial rings causing the polypeptide to curve gently away from the sheet; some are straight. They lack β‐pleat and almost all incorporate a glycine. An example is the first glycine in the GxxxxGK motif of P‐loop proteins. Ribbons in repeating dipeptides can be either flat, as seen in repeated type II and type II′ β‐turns, or twisted, as in multiple type I and type I′ β‐turns. Hexa‐ and octa‐peptides in such twisted ribbons occur frequently in proteins, predominantly with type I β‐turns, and are the same as the “β‐bend ribbons” hitherto identified only in short peptides. One is seen in the GTPase‐activating protein for Rho in the active, but not the inactive, form of the enzyme. It forms a β‐bend ribbon, which incorporates the catalytic arginine, allowing its side chain guanidino group to approach the active site and enhance enzyme activity. Proteins 2014; 82:230–239. © 2013 Wiley Periodicals, Inc.     

Rapid Detection of Mycobacterium tuberculosis by Recombinase Polymerase Amplification

Improved access to effective tests for diagnosing tuberculosis (TB) has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA) is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC) DNA in <20 minutes at 39°C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110) and 20 fg (IS1081)were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9) and 86.1% (95%CI: 78.1, 94.1) respectively (n = 71). Specificities were 100% and 88.6% (95% CI: 80.8, 96.1) respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2) and 70.8% (95%CI: 62.9, 78.7) were obtained (n = 90). Specificities were 95.4 (95% CI: 92.3,98.1) and 88% (95% CI: 83.6, 92.4) respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB assays could be of use for integration into a point-of-care test for use in resource constrained settings.     

Temperature trends and recent decline in body size of the stone marten Martes foina in Denmark

We studied a sample of 131 skulls of the stone marten Martes foina that were collected in Denmark between 1858 and 1999. Data were available for 37 years, but collection effort was not uniform throughout the study period and annual sample size varied between 1 and 27. We used principal component analysis (PCA) to combine the information of four skull measurements into a single variable (PC1). PC1 was then corrected for factors that significantly affected it (sex and longitude), and residual PC1 was used for further analysis in which we calculated trends in PC1 values during the study period. During the study period there was an increase in mean annual temperature in Denmark, but this increase was not continuous, as there was slight decrease in temperature between 1947 and 1965.We found that skull size (and by implication body size) of the stone marten in Denmark had two periods of decrease and these two periods coincide with the periods of increase in mean annual temperature. These results may indicate that body size of the stone marten is sensitive to the change in ambient temperature, either due to a change in food availability that was caused by the increase in temperature, or decreased its size in accordance with Bergmann's rule.     

Prostaglandins and post-abortion luteolysis in early pregnancy.

This study was undertaken to determine if post-abortion luteolysis in early pregnancy could be accelerated by the administration of 15(S)15-methyl-PGF2alpha(15-me-PGF2alpha) or delayed following pretreatment with indomethacin. Thirty-nine women were divided into four groups: 7 women were given 400mug 15-me-PGF2alpha extra-amniotically one hour prior to vacuum aspiration; 14 were pretreated with oral indomethacin (50 mg X4) over 24 hours; 7 were given indomethacin (50mg X 6) over 36 hours and 11 served as controls. Plasma progesterone and estradiol were measured at fixed intervals before and after abortion. There was a rapid drop in the plasma progesterone within the first hour after abortion followed by an exponential decline over the next 23 hours. The plasma estradiol fell rapidly duriing the same period. Under the experimental conditions of this study neither 15-me-PGF2alpha nor indomethacin exerted a significant effect on the decline in luteal function. These results are interpreted as suggesting that factors other than prostaglandins have a more significant role in post-abortion luteolysis.     

The binding sites for tRNA on eukaryotic ribosomes.

We have studied the non-enzymic binding of phe-tRNA to ribosomes from rat liver using deacylated tRNA to inhibit binding to the P-site and puromycin (5 x 10-minus3M) to inhibit binding to the A-site. We conclude that at a low concentration of magnesium ions (10mM) phe-tRNA is bound only at the A-site of 80S irbosomes, whereas at a high concentration of magnesium ions (40mM) phe-tRNA is also bound at the P-site. Studies with edeine indicate that, during non-enzymic binding of phe-tRNA, eukaryotic ribosomes (in contrast to prokarotic ribosomes) have the A-site of the 60S subunit and the initiation site of the 40S subunit juxtaposed. This may account for the differences observed, in formation of diphenylalanyl-tRNA and phenylalanyl-puromycin, between phe-tRNA bound non-enzymically to the P-sites of eukaryotic and prokaryotic ribosomes.     

Prostaglandins and post-abortion luteolysis in early pregnancy

This study was undertaken to determine if post-abortion luteolysis in early pregnancy could be accelerated by the administration of 15(S)15-methyl-PGF_2α (15-me-PGF_2α) or delayed following pretreatment with indomethacin. Thirty-nine women were divided into four groups: 7 women were given 400μg 15-me-PGF_2α extra-amniotically one hour prior to vacuum aspiration; 14 were pretreated with oral indomethacin (50 mg X4) over 24 hours; 7 were given indomethacin (50mg X 6) over 36 hours and 11 served as controls. Plasma progesterone and estradiol were measured at fixed intervals before and after abortion. There was a rapid drop in the plasma progesterone within the first hour after abortion followed by an exponential decline over the next 23 hours. The plasma estradiol fell rapidly during the same period. Under the experimental conditions of this study, neither 15-me-PGF_2α nor indomethacin exerted a significant effect on the decline in luteal function. These results are interpreted as suggesting that factors other than prostaglandins have a more significant role in post-abortion luteolysis.     

Phosphorylation of ribosomal proteins in hamster fibroblasts infected with pseudorabies virus or herpes simplex virus.

In BHK cells infected with pseudorabies virus, there was a substantial increase in the phosphorylation of ribosomal protein S6. This increase occurred between 2 and 4 h after infection and persisted at least until 9 h. We estimated that in mock-infected cells S6 contained, on an average, one phosphate group per protein chain, whereas in infected cells this rose to between four and five phosphate groups per protein chain. A second ribosomal protein, either S16 or S18, was also phosphorylated after infection. No increase in cyclic AMP was found at the time of phosphorylation. We also found an increased phosphorylation of S6 in herpes simplex virus-infected BHK cells.     

Increase in activity of glucose 6-phosphate dehydrogenase in mouse mammary tissue cultured with insulin

1. In organ cultures of mammary tissue from C3H mice we observed increases in the activity of glucose 6-phosphate dehydrogenase similar to that occurring at parturition. 2. In 22hr. cultures of tissue from late-pregnant mice insulin was required for the increases, but the further addition of prolactin, corticosterone and certain other hormones had no effect. The rise in activity occurred over the second half of the culture period. 3. Results from culture of adipose tissue, and mammary tissue rich in adipose tissue, strongly suggest that the rise in activity occurs in mammary parenchymal rather than adipose cells. 4. In 45hr. cultures prolactin prevented a fall in enzyme activity between 22hr. and 45hr. If the medium contained serum the activity at 22hr. was unaffected, but it continued to rise up to 45hr., and prolactin then had no effect. 5. The enzyme also increased in activity in cultures of mammary tissue from mid-pregnant mice. Insulin was again required, the activity was higher at 45hr. than at 24hr. and prolactin increased the activities at both these times. 6. Actinomycin D, cycloheximide and puromycin at low concentration in the media of 22hr. cultures all prevented increases in enzyme activity. Hydroxyurea at a concentration that inhibited the incorporation of [(3)H]thymidine into DNA by 92% had little effect. 7. Actinomycin D and cycloheximide largely failed to prevent the rise in enzyme activity if added after 3.5hr. and 12hr. respectively. Hence all essential RNA and protein synthesis appears to be finished by 3.5hr. and 12hr., although most of the increase in enzyme activity occurs gradually between 12hr. and 22hr. 8. We suggest that the increases in enzyme activity, both in culture and in the living animal at parturition, are induced by an influx of glucose that is restrained during pregnancy by the growth-hormone-like action of placental lactogen.