Structure of the PCBP2/stem–loop IV complex underlying translation initiation mediated by the poliovirus type I IRES

The poliovirus type I IRES is able to recruit ribosomal machinery only in the presence of host factor PCBP2 that binds to stem–loop IV of the IRES. When PCBP2 is cleaved in its linker region by viral proteinase 3CD, translation initiation ceases allowing the next stage of replication to commence. Here, we investigate the interaction of PCBP2 with the apical region of stem–loop IV (SLIVm) of poliovirus RNA in its full-length and truncated form. CryoEM structure reconstruction of the full-length PCBP2 in complex with SLIVm solved to 6.1 Å resolution reveals a compact globular complex of PCBP2 interacting with the cruciform RNA via KH domains and featuring a prominent GNRA tetraloop. SEC-SAXS, SHAPE and hydroxyl-radical cleavage establish that PCBP2 stabilizes the SLIVm structure, but upon cleavage in the linker domain the complex becomes more flexible and base accessible. Limited proteolysis and REMSA demonstrate the accessibility of the linker region in the PCBP2/SLIVm complex and consequent loss of affinity of PCBP2 for the SLIVm upon cleavage. Together this study sheds light on the structural features of the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional interaction is regulated following translation of the poliovirus genome.

DFT study of triplet and singlet elementary acts of acyclic and cyclic alkanes oxidation initiated by primary interaction with 3O2

The primary oxidation stages of 3O2 model acyclic and cyclic alkanes and their subsequent triplet and singlet elementary events were studied for the first time by the DFT method with the density functional B3LYP and basis set 6-311++g(df,p). According to quantum chemical DFT calculations the C–H radical cleavage of the bonds of acyclic and cyclic alkanes upon interaction with 3O2 is almost completely thermodynamically shifted toward the initial state of the reaction system. This energy of primary oxidizing events explains the extremely low reactivity of saturated alkanes in comparison with asphaltene structural fragments under the conditions of SCF technology for the extraction of heavy oils and asphaltenes by a propane-butane mixture. It has been demonstrated that for all elementary acts of primary alkane oxidation the product of the direct reaction direction is not a free pair of radicals but a triplet hydrogen complex with a pronounced hydrogen bond between the hydroperoxyl radical and the radical form of the corresponding hydrocarbon. A new, previously not taken into account very exothermic (H = -29.25 – -30.77 kcal/mol) reaction direction is described which corresponds to triplet recombination of alkyl radicals and a hydroperoxyl radical in its oxygen-concentrated part. The products of this recombination are triplet forms of alkane hydroperoxides in which there is a fairly loosened triplet O---O bond with a length of 2.20-2.23 Å, which is ~0.72-0.77 Å more than bond length in the singlet state.

Latent Radical Cleavage of α-Allenylic C–O Bonds: Potassium Persulfate Mediated Thiolation of Allenylphosphine Oxides

A novel potassium persulfate (K2S2O8) mediated thiolation of allenylphosphine oxides with diaryl sulfides is disclosed. Mechanistic studies indicate that K2S2O8 homolyzes the diaryl sulfide to produce a thiyl radical (PhS•), which is followed by C–O bond cleavage of the allenylphosphine oxide under metal-free conditions, affording novel S,P-bifunctionalized butadienes in moderate to excellent yields.

Oxidative radical divergent Si-incorporation: facile access to Si-containing heterocycles

Oxidative radical cleavage of Si–H/silyl C(sp3)–H bonds, dual Si–H bonds and Si–H/Si–Si bonds toward Si-heterocycles is presented.

Transition-metal-free radical cleavage of a hydrazonyl N–S bond: tosyl radical-initiated cascade C(sp3)–OAr cleavage, sulfonyl rearrangement and atropisomeric cyclopropanation

Combination of 1,10-phenanthroline and potassium carbonate enables a radical cleavage of a hydrazonyl N–S bond, allowing a coupling reaction of N-tosylhydrazone and phosphinyl allene via cascade C–O cleavage, sulfonyl rearrangement and atropisomeric cyclopropanation.

Freedom and friendship in Axel Honneth’s freedom’s right

In Axel Honneth?s Freedom?s Right (FR) personal relations, among which Honneth includes not only family and partner relationships but friendship as well, enable the realization of one ?specific form of freedom, which is difficult to specify? (FR 233). This assertion constitutes one of the main thesis of Freedom?s Right. Accordingly, ?freedom in the sense of individual autonomy? should, among countless different ?conceptions of freedom? be understood as the only one that has the power to shape modern society, while all other values effective within modernity should be understood as ?aspects of the constitutive idea of individual autonomy? (FR 35). In this paper we argue that Honneth?s discussion of the value of friendship does not accomplish its aim for three reasons: first, Honneth is compelled by his argument to postulate one radical cleavage internal to the concept of friendship, by way of an exaggerated contrast between ancient and modern forms of friendship. Second, in his discussion Honneth marginalizes other existing axiologies of friendship, which attribute some other important instrumental, constitutive and final values to this term. Third, even a weaker thesis, one that treats the value of friendship as the precondition of individual freedom as a primus inter pares, seems to lose sight of the central importance that friendship has for us.? Honneth?s key thesis about the unique value of friendship in our society is thereby challenged.

Deuterated nucleotides as chemical probes of RNA structure: a detailed protocol for the enzymatic synthesis of a complete set of nucleotides specifically deuterated at ribose carbons

We describe here a detailed protocol for the synthesis of ribonucleotides specifically deuterated at each ribose carbon atom. We synthesized 20 specifically deuterated ribonucleotides: ATP, CTP, GTP, and UTP, each of which contained one of five deuterated riboses (either 1′-D, 2″-D, 3′-D, 4′-D, or 5′,5″-D2). Our synthetic approach is inspired by the pioneering work of Tolbert and Williamson, who developed a method for the convenient one-pot enzymatic synthesis of nucleotides (Tolbert, T. J. and Williamson, J. R. (1996) J. Am. Chem. Soc. 118, 7929–7940). Our protocol consists of a comprehensive list of required chemical and enzymatic reagents and equipment, detailed procedures for enzymatic assays and nucleotide synthesis, and chromatographic procedures for purification of deuterated nucleotides. As an example of the utility of specifically deuterated nucleotides, we used them to synthesize specifically deuterated sarcin/ricin loop (SRL) RNA and measured the deuterium kinetic isotope effect on hydroxyl radical cleavage of the SRL.