Asymmetric deceleration of ClpB or Hsp104 ATPase activity unleashes protein-remodeling activity

Two members of the AAA+ superfamily, ClpB and Hsp104, collaborate with Hsp70 and Hsp40 to rescue aggregated proteins. However, the mechanisms that elicit and underlie their protein-remodeling activities remain unclear. We report that for both Hsp104 and ClpB, mixtures of ATP and ATP-gammaS unexpectedly unleash activation, disaggregation and unfolding activities independent of cochaperones. Mutations reveal how remodeling activities are elicited by impaired hydrolysis at individual nucleotide-binding domains. However, for some substrates, mixtures of ATP and ATP-gammaS abolish remodeling, whereas for others, ATP binding without hydrolysis is sufficient. Remodeling of different substrates necessitates a diverse balance of polypeptide 'holding' (which requires ATP binding but not hydrolysis) and unfolding (which requires ATP hydrolysis). We suggest that this versatility in reaction mechanism enables ClpB and Hsp104 to reactivate the entire aggregated proteome after stress and enables Hsp104 to control prion inheritance.     

Finding a common motif of RNA sequences using genetic programming: the GeRNAMo system

We focus on finding a consensus motif of a set of homologous or functionally related RNA molecules. Recent approaches to this problem have been limited to simple motifs, require sequence alignment, and make prior assumptions concerning the data set. We use genetic programming to predict RNA consensus motifs based solely on the data set. Our system -- dubbed GeRNAMo (Genetic programming of RNA Motifs) -- predicts the most common motifs without sequence alignment and is capable of dealing with any motif size. Our program only requires the maximum number of stems in the motif, and if prior knowledge is available the user can specify other attributes of the motif (e.g., the range of the motif's minimum and maximum sizes), thereby increasing both sensitivity and speed. We describe several experiments using either ferritin iron response element (IRE); signal recognition particle (SRP); or microRNA sequences, showing that the most common motif is found repeatedly, and that our system offers substantial advantages over previous methods.     

Chiral separation of aliphatic primary amino alcohols as o‐phthaldialdehyde/mercaptoethanol derivatives on polysaccharide‐based chiral stationary phases

A sensitive chiral high performance liquid chromatography (HPLC) method for the determination of aliphatic primary amino alcohol isomers with o‐phthaldialdehyde/mercaptoethanol precolumn derivatization has been developed and validated. Seven chiral columns were tested in a reversed phase mode. Excellent enantioseparation with the resolution more than 2.0 was achieved on Chiralcel OJ‐3R. The effect of various chromatographic conditions including column temperature, acetonitrile content in the mobile phase, buffer pH, buffer concentration, and buffer type in the mobile phase on the retention and the selectivity was investigated. The final mobile phase consisted of binary mixture of 20mM ammonium formate solution with acetonitrile (75:25; v/v). The analyses were performed at mobile phase flow rate of 1.0 mL/min and the column temperature of 40°C. The fluorescence detection was performed at excitation wavelength of 345 nm and emission wavelength of 450 nm. The developed method was fully validated in terms of linearity, sensitivity, accuracy, precision, intermediate precision, and selectivity according to International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use guidelines using internal normalization procedure. The proposed chiral method was proved to be highly sensitive, simple, and rapid and was successfully applied to the determination of D‐Valinol content in commercially available samples of L‐Valinol.     

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.     

Proteins reacting with anti-spectrin antibodies are present in Chlamydomonas cells.

It was found either in Western-blot analysis or in indirect immunofluorescence microscopy that cells of the alga Chlamydomonas reinhardtii contain polypeptides cross-reacting with antibodies directed against red blood cell spectrin. The protein could also be detected by immunoprecipitation with anti-spectrin antibodies. C. reinhardtii cells contain distinct polypeptide chains reacting with antibodies directed against either α- or β-spectrin subunits. This protein was extracted from the cells with low ionic strength solution but was not with nonionic detergent.     

In vitro glycosidation potential towards olomoucine-type cyclin-dependent kinase inhibitors in rodent and primate microsomes

Interspecies differences in glycosidation potential in mammalian tissues represent a factor contributing to ambiguity when endobiotic and/or xenobiotic metabolic pathways are extrapolated from animals to man. Using the TLC/autoradiographic technique, we conducted an in vitro investigation involving mouse, rat, monkey, as well as human liver and kidney microsomes to evaluate their glycoconjugation potential towards (3)H-labeled, purine-derived selective inhibitors of cyclin-dependent kinases such as olomoucine, bohemine, roscovitine, 6-(2-hydroxybenzyl)amino-2-(1-hydroxymethyl-2-methylpropyl)amino-9-isopropylpurine (compound A-4), and 6-(3-hydroxybenzyl)amino-2-[(1(R/S)-hydroxymethyl)propyl]amino-9-isopropylpurine (compound A-5) as aglycones. Principally, this study confirmed the aliphatic hydroxyl group of olomoucine-type inhibitors as a relatively suitable target for glucuronide, glucoside, xyloside, galactoside, and/or N-acetylaminoglucoside conjugation. Of the tissues examined, only the mouse microsomes were able to perform glucosidation and galactosidation reactions with the aglycones. On the other hand, monkey microsomes were superior to the mouse microsomes in a variety of glucuronide conjugates produced with compounds A-4 and A-5.     

The content of four immunomodulatory steroids and major androgens in human semen

Seminal fluid fulfils a dual role: it provides optimal conditions for fertilization and protects male germ cells from infections. Besides both major sexual hormones and cortisol it contains a considerable amounts of dehydroepiandrosterone (DHEA), known to counteract the excessive actions of glucocorticoids. From this point of view of importance may be our recent finding of both 7-hydroxy-dehydroepiandrosterone epimers (7-OH-DHEA) in semen, believed to be in some instances the locally active immunoprotective agents. The concentrations of these steroids were of the same range or even higher than in blood. Here further data on 7-OH-DHEA in semen, along with other relevant steroid hormones, are given in 79 samples, either from healthy males or from patients with various sexual disorders. A method has been developed enabling us a simultaneous determination of DHEA, 7-OH-DHEA epimers, testosterone, dihydrotestosterone and cortisol in seminal fluid. It was based on ether extraction, solvent partition and HPLC separation, followed by specific radioimmunoassays in the respective fractions. In addition, the steroids were measured in serum and the concentrations in both fluids were compared. The concentrations of 7-OH-DHEA in seminal fluid varied from 1.8 to 15.7 nmol/l, while those of DHEA were about five times higher.