The free energy folding penalty accompanying binding of intrinsically disordered α‐helical motifs

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes and preform critical roles in many cellular processes, most often through the association with globular proteins. Despite lacking a stable three‐dimensional structure by themselves, they may acquire a defined conformation upon binding globular targets. The most common type of secondary structure acquired by these binding motifs entails formation of an α‐helix. It has been hypothesized that such disorder‐to‐order transitions are associated with a significant free energy penalty due to IDP folding, which reduces the overall IDP‐target affinity. However, the exact magnitude of IDP folding penalty in α‐helical binding motifs has not been systematically estimated. Here, we report the folding penalty contributions for 30 IDPs undergoing folding‐upon‐binding and find that the average IDP folding penalty is +2.0 kcal/mol and ranges from 0.7 to 3.5 kcal/mol. We observe that the folding penalty scales approximately linearly with the change in IDP helicity upon binding, which provides a simple empirical way to estimate folding penalty. We analyze to what extent do pre‐structuring and target‐bound IDP dynamics (fuzziness) reduce the folding penalty and find that these effects combined, on average, reduce the folding cost by around half. Taken together, the presented analysis provides a quantitative basis for understanding the role of folding penalty in IDP‐target interactions and introduces a method estimate this quantity. Estimation and reduction of IDP folding penalty may prove useful in the rational design of helix‐stabilized inhibitors of IDP‐target interactions.StatementThe α‐helical binding motifs are ubiquitous among the intrinsically disordered proteins (IDPs). Upon binding their targets, they undergo a disorder‐to‐order transition, which is accompanied by a significant folding penalty whose magnitude is generally not known. Here, we use recently developed statistical‐thermodynamic model to estimate the folding penalties for 30 IDPs and clarify the roles of IDP pre‐folding and bound‐state dynamics in reducing the folding penalty.     

Development and validation of a liquid chromatography-tandem mass spectrometry assay for determination of raloxifene and its metabolites in human plasma

This paper describes the development and validation of a method for the detection of raloxifene (Ral) and its two glucuronide metabolites, raloxifene-6-glucuronide (M1) and raloxifene-4'-glucuronide (M2), in human plasma samples. Both glucuronides were synthesized enzymatically, purified and used as authentic standards. The assay involves a simple solid phase extraction (SPE) procedure of 0.5 mL of human plasma and subsequent analysis by LC-MS-MS. The recoveries were higher than 71% and chromatographic separation of all the analytes was accomplished in less than 7 min. Linear ranges (r(2)>0.99) were found from 0.200 to 340 microg/L, from 1.600 to 2720 microg/L and from 0.088 to 60.00 microg/L, for M1, M2 and Ral, respectively. The limits of detection achieved were 8, 11 and 6 ng/L for M1, M2 and Ral, respectively. The method presented was successfully applied to a genetic polymorphism study of 47 plasma samples from women taking Evista (raloxifene hydrochloride).     

Engrafting fetal liver cells into multiple tissues of healthy adult mice without the use of immunosuppressants

We have shown the fetal liver cell engraftments into multiple tissues of adult healthy mice, achieved without suppressing the animals’ immune systems. Fetal cells from the livers of male C57Bl/6J Black lineage mice at day 13 to 15 of gestation were injected intravenously into female adult CC57W/MY White mice. The grafting was evaluated by Y-chromosome-specific PCR, cytometric analysis of fluorescently stained donor cells, and histological analysis. All the methods consistently showed the presence of multiple engraftments randomly distributed through the various organs of the recipients. After 60 days, the grafts still constituted 0.1 to 2.75% of the tissues. The grafted cells did not change their appearance in any of the organs except the brain, where they became enlarged. Inflammatory reactions were not detected in any of the histological preparations. The frequency of engraftments was higher in the liver, indicating that similarity between the donor and recipient cells facilitates engraftment. The high inherent plasticity of fetal liver cells underlies their ability to integrate into healthy recipient organs, which can be governed by environmental conditions and connections with neighboring cells rather than by the initial cellular developmental programs. The fact that fetal liver cells can be grafted into multiple tissues of healthy animals indicates that they can be used to replace the natural loss of cells in adult organisms.     

Alternative interactions define gyrase specificity in the CcdB family

Toxin-antitoxin (TA) modules are small operons associated with stress response of bacteria. F-plasmid CcdB(F) was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved residues crucial for gyrase poisoning activity of plasmidic CcdBs are not conserved among these families. Here we show that the chromosomal CcdB(Vfi) from Vibrio fischeri is an active gyrase poison that interacts with its target via an alternative energetic mechanism. Changes in the GyrA14-binding surface of the Vibrio and F-plasmid CcdB family members illustrate neutral drift where alternative interactions can be used to achieve the same functionality. Differences in affinity between V. fischeri and F-plasmid CcdB for gyrase and their corresponding CcdA antitoxin possibly reflect distinct roles for TA modules located on plasmids and chromosomes.     

Synthesis and Structural Characterization of Novel Camphor-derived Amines

Two novel 4‐substituted camphidine derivatives 10a , b have been prepared from (+)‐camphor ( 1 ) in five steps, the Beckmann rearrangement being the bottleneck of the synthesis. Isoborneol derivative 5b , formed as a side product during the hydrogenation of arylidene ketone 3b , under Beckmann rearrangement conditions yielded interesting novel rearrangement products 11 and 12 . (1S)‐(+)‐Camphorquinone ( 13 ) was transformed into diamines 15 and 16 in two steps, the former being cyclized into an imidazoline salt 17 , an N‐heterocyclic carbene precursor. The structures of all novel compounds have been meticulously characterized using NMR techniques and/or single crystal X‐ray analysis. Chirality 24:778–788, 2012. © 2012 Wiley Periodicals, Inc.     

Determination of raloxifene and its glucuronides in human urine by liquid chromatography-tandem mass spectrometry assay

A selective, sensitive, accurate and precise liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for determination of raloxifene and its three glucuronides: raloxifene-6-β-glucuronide (M1), raloxifene-4'-β-glucuronide (M2), raloxifene-6,4'-diglucuronide (M3) in urine samples is presented in this paper. To our knowledge the developed analytical method is the first fully validated method capable of simultaneous determination of raloxifene and its glucuronides in real urine samples. Moreover, for the first time a method for determination of raloxifene diglucuronide in relevant biological samples was introduced. Metabolites were obtained by a bioconversion process of raloxifene to its glucuronides using the microorganism Streptomyces sp. and were used as standards for validation. Urine samples were introduced to a simple solid phase extraction prior to the analysis by LC-MS/MS. The method was linear in a wide range with high determination coefficient (r(2) > 0.997). The limits of quantification achieved were 1.01, 1.95, 2.83 and 4.69 nM for raloxifene, M1, M2 and M3, respectively. The recoveries were higher than 92.5%, the accuracy was within 100 ± 8.8% and the precision was better than 12% for all compounds. The developed method was successfully applied to the real urine samples and showed to be appropriate for use in further research of still not completely discovered raloxifene pharmacokinetics. Furthermore, the presented method could also serve for a potential application in anti-doping analysis.     

Chromatography-mass spectrometry studies on the metabolism of synthetic cannabinoids JWH-018 and JWH-073, psychoactive components of smoking mixtures

The Russian Federation prohibited the distribution of herbal mixtures with synthetic aminoalkylindoles JWH-018 and JWH-073, agonist cannabinoid receptors, on January 22, 2010. The lack or low content of their native compounds in urine requires detailed identification of their metabolites, which are excreted with urine and are present in blood. Using gas and liquid chromatography-mass spectrometry, we identified a series of metabolites in urine samples from humans and rats that were products of the following reactions: (a) mono- and dihydroxylation of the parent compounds with hydroxyl groups located at aromatic and aliphatic residues, (b) carboxylation, (c) N-dealkylation and (d) N-dealkylation and hydroxylation. The prevailing urinary metabolites in humans are monohydroxylated forms, while N-dealkylated and N-dealkyl monohydroxylated forms are found in rats. Twenty-six samples of herbal smoking mixtures with JWH-018, purchased in Russia, were analysed.     

Diurnal Variations in the Motility of Populations of Biflagellate Microalgae

The motility of microalgae has been studied extensively, particularly in model microorganisms such as Chlamydomonas reinhardtii. For this and other microalgal species, diurnal cycles are well known to control the metabolism, growth, and cell division. Diurnal variations, however, have been largely neglected in quantitative studies of motility. Here, we demonstrate using tracking microscopy how the motility statistics of C. reinhardtii are modulated by diurnal cycles. With nine independently inoculated cultures synchronized to the light-dark cycle at the exponential growth phase, we repeatedly observed that the mean swimming speed is greater during the dark period of a diurnal cycle. From this measurement, using a hydrodynamic power balance, we infer the mean flagellar beat frequency and conjecture that its diurnal variation reflects modulation of intracellular ATP. Our measurements also quantify the diurnal variations of the orientational and gravitactic transport of C. reinhardtii. We use this to explore the population-level consequences of diurnal variations of motility statistics by evaluating a prediction for how the gravitactic steady state changes with time during a diurnal cycle. Finally, we discuss the consequences of diurnal variations of microalgal motility in soil and pelagic environments.