Partitioning of tRNA-dependent Editing between Pre- and Post-transfer Pathways in Class I Aminoacyl-tRNA Synthetases

Hydrolytic editing activities are present in aminoacyl-tRNA synthetases possessing reduced amino acid discrimination in the synthetic reactions. Post-transfer hydrolysis of misacylated tRNA in class I editing enzymes occurs in a spatially separate domain inserted into the catalytic Rossmann fold, but the location and mechanisms of pre-transfer hydrolysis of misactivated amino acids have been uncertain. Here, we use novel kinetic approaches to distinguish among three models for pre-transfer editing by Escherichia coli isoleucyl-tRNA synthetase (IleRS). We demonstrate that tRNA-dependent hydrolysis of noncognate valyl-adenylate by IleRS is largely insensitive to mutations in the editing domain of the enzyme and that noncatalytic hydrolysis after release is too slow to account for the observed rate of clearing. Measurements of the microscopic rate constants for amino acid transfer to tRNA in IleRS and the related valyl-tRNA synthetase (ValRS) further suggest that pre-transfer editing in IleRS is an enzyme-catalyzed activity residing in the synthetic active site. In this model, the balance between pre-transfer and post-transfer editing pathways is controlled by kinetic partitioning of the noncognate aminoacyl-adenylate. Rate constants for hydrolysis and transfer of a noncognate intermediate are roughly equal in IleRS, whereas in ValRS transfer to tRNA is 200-fold faster than hydrolysis. In consequence, editing by ValRS occurs nearly exclusively by post-transfer hydrolysis in the editing domain, whereas in IleRS both pre- and post-transfer editing are important. In both enzymes, the rates of amino acid transfer to tRNA are similar for cognate and noncognate aminoacyl-adenylates, providing a significant contrast with editing DNA polymerases.     

Bypass of a nick by the replisome of bacteriophage T7

DNA polymerase and DNA helicase are essential components of DNA replication. The helicase unwinds duplex DNA to provide single-stranded templates for DNA synthesis by the DNA polymerase. In bacteriophage T7, movement of either the DNA helicase or the DNA polymerase alone terminates upon encountering a nick in duplex DNA. Using a minicircular DNA, we show that the helicase · polymerase complex can bypass a nick, albeit at reduced efficiency of 7%, on the non-template strand to continue rolling circle DNA synthesis. A gap in the non-template strand cannot be bypassed. The efficiency of bypass synthesis depends on the DNA sequence downstream of the nick. A nick on the template strand cannot be bypassed. Addition of T7 single-stranded DNA-binding protein to the complex stimulates nick bypass 2-fold. We propose that the association of helicase with the polymerase prevents dissociation of the helicase upon encountering a nick, allowing the helicase to continue unwinding of the duplex downstream of the nick.     

Metal complexes with the quinolone antibacterial agent N-propyl-norfloxacin: synthesis, structure and bioactivity

Nine new metal complexes of the quinolone antibacterial agent N-propyl-norfloxacin, pr-norfloxacin, with VO(2+), Mn(2+), Fe(3+), Co(2+), Ni(2+), Zn(2+), MoO(2)(2+), Cd(2+) and UO(2)(2+) have been prepared and characterized with physicochemical and spectroscopic techniques while molecular mechanics calculations for Fe(3+), VO(2+) and MoO(2)(2+) complexes have been performed. In all complexes, pr-norfloxacin acts as a bidentate deprotonated ligand bound to the metal through the pyridone and one carboxylate oxygen atoms. All complexes are six-coordinate with slightly distorted octahedral geometry. For the complex VO(N-propyl-norfloxacinato)(2)(H(2)O) the axial position, trans to the vanadyl oxygen, is occupied by one pyridone oxygen atom. The investigation of the interaction of the complexes with calf-thymus DNA has been performed with diverse spectroscopic techniques and has shown that the complexes can be bound to calf-thymus DNA resulting to a B-->A DNA transition. The antimicrobial activity of the complexes has been tested on three different microorganisms. The complexes show equal or decreased biological activity in comparison to the free pr-norfloxacin except UO(2)(pr-norf)(2) which shows better inhibition against S. aureus.     

Spectroscopic, viscositic and electrochemical studies of DNA interaction with a novel mixed-ligand complex of nickel (II) that incorporates 1-methylimidazole and thiocyanate groups

A novel mixed-ligand nickel(II) complex that contains 1-methylimidazole and thiocyanate, Ni(NCS)(2)(Mim)(4) (Mim=1-methylimidazole), was synthesized and its structure was determined by X-ray crystallography, IR spectrum and elemental analysis, etc. Its DNA-binding properties were studied by electronic absorption spectral, viscositive and electrochemical measurements. The absorption spectral and viscositive results suggest that the nickel(II) complex binds to DNA via partial intercalation. The addition of DNA results in the decrease of the peak current of the nickel(II) complex proved their interaction. The slight differences of peak profiles and electrochemical parameters between free and DNA-bound Ni(NCS)(2)(Mim)(4) showed the formation of an electrochemical inactive complex between Ni(NCS)(2)(Mim)(4) and DNA. The binding site and binding constant of the complex to DNA were determined by electrochemical titration method.     

Food web structure and interaction strength pave the way for vulnerability to extinction

This paper focuses on how food web structure and interactions among species affects the vulnerability, due to environmental variability, to extinction of species at different positions in model food webs. Vulnerability is here not measured by a traditional extinction threshold but is instead inspired by the IUCN criteria for endangered species: an observed rapid decline in population abundance. Using model webs influenced by stochasticity with zero autocorrelation, we investigate the ecological determinants of species vulnerability, i.e. the trophic interactions between species and food web structure and how these interact with the risk of sudden drops in abundance of species. We find that (i) producers fulfil the criterion of vulnerable species more frequently than other species, (ii) food web structure is related to vulnerability, and (iii) the vulnerability of species is greater when involved in a strong trophic interaction than when not. We note that our result on the relationship between extinction risk and trophic position of species contradict previous suggestions and argue that the main reason for the discrepancy probably is due to the fact that we study the vulnerability to environmental stochasticity and not extinction risk due to overexploitation, habitat destruction or interactions with introduced species. Thus, we suggest that the vulnerability of species to environmental stochasticity may be differently related to trophic position than the vulnerability of species to other factors. Earlier research on species extinctions has looked for intrinsic traits of species that correlate with increased vulnerability to extinction. However, to fully understand the extinction process we must also consider that species interactions may affect vulnerability and that not all extinctions are the result of long, gradual reductions in species abundances. Under environmental stochasticity (which importance frequently is assumed to increase as a result of climate change) and direct and indirect interactions with other species some extinctions may occur rapidly and apparently unexpectedly. To identify the first declines of population abundances that may escalate and lead to extinctions as early as possible, we need to recognize which species are at greatest risk of entering such dangerous routes and under what circumstances. This new perspective may contribute to our understanding of the processes leading to extinction of populations and eventually species. This is especially urgent in the light of the current biodiversity crisis where a large fraction of the world's biodiversity is threatened.     

Sexually mature and immature yearling male European ground squirrels: a comparison of behavioral and physiological parameters

Early puberty may increase lifetime reproductive success, but may also entail diverse costs. In male European ground squirrels (Spermophilus citellus), age at sexual maturity varies among individuals. We compared sexually active and inactive yearling males under standardized conditions in outdoor enclosures. Non-reproductive yearling males hibernated significantly longer than mature males and emerged when the mating period had already started. Testosterone concentrations peaked in the precocious males during premating and mating, and were depressed in the non-reproductive individuals throughout the study period. Emergence body mass was similar in both groups, although sexually immature males were significantly heavier at the end of the active season. Additionally, non-reproductive yearlings grew faster than precocious individuals. Male–male aggression peaked during mating and the following 4 weeks. Intense aggressive interactions like chases and fights were mostly initiated by reproductive males and were directed towards mature competitors. Aggressive behavior in immature males was mainly expressed as spatial displacements. Non-agonistic interactions with females were only observed in sexually active males. Concentrations of fecal cortisol metabolites did not differ between the two male groups and were elevated in the second half of the active season. Leucocyte numbers were reduced during mating in mature males, whereas in immature animals, cell numbers did not change significantly. Our results indicate that early puberty in European ground squirrels involves lower growth rates, high intrasexual aggression, lower prehibernatory body mass, and probably worse immunological condition during mating.     

Mononuclear copper(II) complexes with quinolones and nitrogen-donor heterocyclic ligands: Synthesis, characterization, biological activity and interaction with DNA

The neutral mononuclear copper(II) complexes with the quinolone antibacterial drugs, pipemidic acid and N-propyl-norfloxacin, in the presence or absence of nitrogen-donor heterocyclic ligands, 2,2′-bipyridine, 1,10-phenanthroline or 2,2′-dipyridylamine, have been prepared and characterized spectroscopically. The interaction of copper(II) with the deprotonated quinolone ligand leads to the formation of the neutral mononuclear complexes of the type [Cu(quinolone)₂(H₂O)] (1)–(2) while the presence of the N-donor ligand leads to the formation of the neutral mononuclear complexes of the type [Cu(quinolone)(N-donor)Cl] (3)–(8). In all the complexes, copper(II) is pentacoordinate having a distorted square pyramidal geometry. The electron paramagnetic resonance spectra of 1 and 2 are typical of mononuclear Cu(II) complexes, while for the mixed-ligands complexes 3–8 a mixture of dimeric and monomeric species is indicated. The interaction of the complexes with calf-thymus DNA has been investigated with diverse spectroscopic techniques and has shown that the complexes can be bound to calf-thymus DNA by the intercalative mode. The antimicrobial activity of the complexes has been tested on three different microorganisms. All the complexes show an increased biological activity in comparison to the corresponding free quinolone ligand.     

Surface plasmon resonance for probing quadruplex folding and interactions with proteins and small molecules

Surface plasmon resonance is a technique for detecting binding events at the surface of a thin metal film. Through the commercial availability of instrumentation and sensor chips, the technique has found widespread application for determining the affinity and kinetics of macromolecular interactions. A variety of quadruplex forming oligonucleotides have been immobilized to sensor chips to permit analysis of their binding interactions with both small molecule and protein analytes. The fold of the quadruplex must be maintained through an appropriate choice of buffer, and care must be taken to ensure that data interpretation is not hampered by non-specific binding and adsorption of the analyte to the sensor surface and instrument. Affinity constants determined by surface plasmon resonance for interactions with quadruplexes correlate meaningfully with other methods, such as UV-visible and fluorescence titrations, enzyme linked immunosorbent assay, thermal melting studies and telomerase inhibition. Kinetic measurements of the association and dissociation of duplexes of quadruplex forming oligonucleotides and their complementary strands have enabled calculation of the folding and unfolding rates of the quadruplex itself, and determination of its stability as a function of buffer composition.     

The CD44 standard/ezrin complex regulates Fas-mediated apoptosis in Jurkat cells

The transmembrane receptor CD44 conveys important signals from the extracellular microenvironment to the cytoplasm, a phenomena known as “outside-in” signaling. CD44 exists as several isoforms that result from alternative splicing, which differ only in the extracellular domain but yet exhibit different activities. CD44 is a binding partner for the membrane-cytoskeleton cross-linker protein ezrin. In this study, we demonstrate that only CD44 standard (CD44s) colocalizes and interacts with the actin cross-linkers ezrin and moesin using well-characterized cell lines engineered to express different CD44 isoforms. Importantly, we also show that the association CD44s-ezrin-actin is an important modulator of Fas-mediated apoptosis. The results highlight a mechanism by which signals from the extracellular milieu regulate intracellular signaling activities involved in programmed cell death. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Fragment molecular orbital calculations for biomolecules

Exploring biomolecule behavior, such as proteins and nucleic acids, using quantum mechanical theory can identify many life science phenomena from first principles. Fragment molecular orbital (FMO) calculations of whole single particles of biomolecules can determine the electronic state of the interior and surface of molecules and explore molecular recognition mechanisms based on intermolecular and intramolecular interactions. In this review, we summarized the current state of FMO calculations in drug discovery, virology, and structural biology, as well as recent developments from data science.