Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.     

Bi-enzyme L-arginine-selective amperometric biosensor based on ammonium-sensing polyaniline-modified electrode

A novel L-arginine-selective amperometric bi-enzyme biosensor based on recombinant human arginase I isolated from the gene-engineered strain of methylotrophic yeast Hansenula polymorpha and commercial urease is described. The biosensing layer was placed onto a polyaniline-Nafion composite platinum electrode and covered with a calcium alginate gel. The developed sensor revealed a good selectivity to L-arginine. The sensitivity of the biosensor was 110 ± 1.3 nA/(mM mm(2)) with the apparent Michaelis-Menten constant (K(M)(app)) derived from an L-arginine (L-Arg) calibration curve of 1.27 ± 0.29 mM. A linear concentration range was observed from 0.07 to 0.6mM, a limit of detection being 0.038 mM and a response time - 10s. The developed biosensor demonstrated good storage stability. A laboratory prototype of the proposed amperometric biosensor was applied to the samples of three commercial pharmaceuticals ("Tivortin", "Cytrarginine", "Aminoplazmal 10% E") for L-Arg testing. The obtained L-Arg-content values correlated well with those declared by producers.     

Effect of local sugar and base geometry on <Superscript>13</Superscript>C and <Superscript>15</Superscript>N magnetic shielding anisotropy in DNA nucleosides

Density functional theory was employed to study the dependence of 13C and 15N magnetic shielding tensors on the glycosidic torsion angle (chi) and conformation of the sugar ring in 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine. In general, the magnetic shielding of the glycosidic nitrogens and the sugar carbons was found to depend on both the conformation of the sugar ring and chi. Our calculations indicate that the magnetic shielding anisotropy of the C6 atom in pyrimidine and the C8 atom in purine bases depends strongly on chi. The remaining base carbons were found to be insensitive to both sugar pucker and chi re-orientation. These results call into question the underlying assumptions of currently established methods for interpreting residual chemical shift anisotropies and 13C and 15N auto- and cross-correlated relaxation rates and highlight possible limitations of DNA applications of these methods.     

Site-specific recombinases in genetic engineering: Modern in vivo technologies

A review was conducted over the current achievements in the area of site-specific recombinases (SSR) and their applications for manipulations with pro- and eukaryotic genomes. The principles of SSR functioning and the types of genetic rearrangements catalyzed by SSR were analyzed. The examples given in this review show the SSR potential to solve a wide range of basic and practical problems. To use different methods for solving these problems, however, would be more difficult or even impossible. The main directions for further developing the technology of site-specific recombination are the following: the use of SSR for a wider range of biological systems; generation of the SSR, which are characterized by strictly controlled expression in space and time; and the search for recombinases with new substrate specificity.     

Effect of microbial activity on buried cyanobacterial organic matter

The biomass from which hydrocarbons were formed and the organisms responsible for its production are usually deduced by the use of biochemical markers. In the present study, using a simulated sedimentary system, cyanobacterial organic matter was buried in sediments and exposed to sequential environmental changes ranging from microaerobic conditions at ambient temperature to strongly reducing conditions at a biologically extreme temperature and pressure. Significant changes occurred in the composition of hydrocarbons and fatty acids isolated from the biomass that masked the characteristic patterns exhibited by the original cyanobacterial material. The changes depended on the particular environmental conditions to which the organic matter was exposed. The results stress the need for caution in interpreting biochemical markers in terms of their source material in sediments.     

Potential range of impact of an ecological trap network: the case of timber stacks and the Rosalia longicorn

Although the negative impact of timber stacks on populations of saproxylic beetles is a well-known phenomenon, there is relatively little data concerning the scale of this impact and its spatial aspect. Beech timber stored in the vicinity of the forest can act as an ecological trap for the Rosalia longicorn (Rosalia alpina), so in this study we have attempted to determine the spatial range of the impact of a network of timber stacks. Timber stacks in the species’ range in the study area were listed and monitored during the adult emergence period in 2014–2016. Based on published data relating to the species’ dispersal capabilities, buffers of four radii (500, 1000, 1600, 3000 m) were delineated around the stacks and the calculated ranges of potential impact. The results show that the percentage of currently known localities of the Rosalia longicorn impacted by stacks varies from 19.7 to 81.6%, depending on the assumed impact radius. The percentage of forest influenced by timber stacks was 77% for the largest-radius buffer. The overall impact of the ecological trap network is accelerated by fragmentation of the impact-free area. It was also found that forests situated close to the timber stacks where the Rosalia longicorn was recorded were older and more homogeneous in age and species composition than those around stacks where the species was absent. Such results suggest that timber stacks act as an ecological trap in the source area of the local population.     

Enhancer Activation by Pharmacologic Displacement of LSD1 from GFI1 Induces Differentiation in Acute Myeloid Leukemia

1. Download high-res image (244KB)
2. Download full-size image

     

Isoenzymes of hypoxanthine-guanine-phosphoribosyl transferase in a family with partial deficiency of the enzyme

The isoenzymes of hypoxanthine-guanine-phosphoribosyl transferase (HGPRT; E. C. 2.4.2.8) were studied by polyacrylamide gel disc electrophoresis in the erythrocytes of a family in which there was a partial deficiency of this X-linked enzyme. Hyperuricemic males, in whom HGPRT activity was 4% of normal, were found to have a variant enzyme which had altered kinetic and electrophoretic properties. In acrylamide gel, this variant migrated about 15% faster than the normal enzyme, and its K _m for hypoxanthine was twice that of the normal. The sister of two patients had 34% of normal activity in her erythrocytes and was thought to be a heterozygote. Electrophoresis of her hemolysate yielded profiles in which there were two zones of HGPRT activity. The more slowly migrating isoenzyme behaved electrophoretically like the normal isoenzyme. The faster-migrating isoenzyme had a mobility identical to that of the variant enzyme found in hemolysates from her hyperuricemic siblings. However, in her profile the activity of the variant enzyme was three times greater than that of the HGPRT found in the boys. This increased activity appears to be due to an interaction of the variant enzyme with the normal enzyme. Electrophoresis of a mixture of normal enzyme and the variant from a hyperuricemic male yielded a profile similar to that observed in this girl and a dramatic increase in the amount of activity in the variant zone.Aided by U.S. Public Health Service Grants No. HD04608 and GM 17702 from the National Institute of Child Health and Human Development and from the National Institute of General Medical Sciences, respectively, National Institutes of Health. Presented in part at the 1971 Annual Meeting of the Western Society for Pediatric Research, Carmel, California.