Membrane-mediated induction and sorting of K-Ras microdomain signaling platforms

The K-Ras4B GTPase is a major oncoprotein whose signaling activity depends on its correct localization to negatively charged subcellular membranes and nanoclustering in membrane microdomains. Selective localization and clustering are mediated by the polybasic farnesylated C-terminus of K-Ras4B, but the mechanisms and molecular determinants involved are largely unknown. In a combined chemical biological and biophysical approach we investigated the partitioning of semisynthetic fully functional lipidated K-Ras4B proteins into heterogeneous anionic model membranes and membranes composed of viral lipid extracts. Independent of GDP/GTP-loading, K-Ras4B is preferentially localized in liquid-disordered (l(d)) lipid domains and forms new protein-containing fluid domains that are recruiting multivalent acidic lipids by an effective, electrostatic lipid sorting mechanism. In addition, GDP-GTP exchange and, thereby, Ras activation results in a higher concentration of activated K-Ras4B in the nanoscale signaling platforms. Conversely, palmitoylated and farnesylated N-Ras proteins partition into the l(d) phase and concentrate at the l(d)/l(o) phase boundary of heterogeneous membranes. Next to the lipid anchor system, the results reveal an involvement of the G-domain in the membrane interaction process by determining minor but yet significant structural reorientations of the GDP/GTP-K-Ras4B proteins at lipid interfaces. A molecular mechanism for isoform-specific Ras signaling from separate membrane microdomains is postulated from the results of this study.     

Hyperaromatic stabilization of arenium ions: a remarkable cis stereoselectivity of nucleophilic trapping of β-hydroxyarenium ions by water

Cis- and trans-1,2-dihydrodiol isomers of benzene undergo acid-catalyzed dehydration to form phenol. In principle the isomeric substrates react through a common β-hydroxybenzenium (cyclohexadienyl) carbocation. Notwithstanding, the isomers show a large difference in reactivity, k(cis)/k(trans) = 4500. This difference is reduced to k(cis)/k(trans) = 440 and 50 for the 1,2-dihydrodiols of naphthalene and 9,10-dihydrodiols of phenanthrene, respectively, and to 6.9 for the dihydrodiols of the nonaromatic 7,8-double bond of acenaphthylene. Because the difference in stabilities of cis- and trans-dihydrodiols should be no more than 2-3-fold, these results imply a high cis stereoselectivity for nucleophilic trapping of a β-hydroxyarenium cation by water in the reverse of the carbocation-forming reaction. This is confirmed by studies of the 10-hydroxy-9-phenanthrenium ion generated from aqueous solvolyses of the trans-9,10-bromohydrin derivative of phenanthrene and the monotrichloroacetate ester of the phenanthrene cis-9,10-dihydrodiol. The cis stereoselectivity of forward and reverse reactions is explained by the formation (in the "forward" reaction) of different conformations of carbocation from cis- and trans-dihydrodiol reactants with respectively β-C-H and β-C-OH bonds in pseudoaxial positions with respect to the charge center of the carbocation optimal for hyperconjugation. Formation of different conformations is constrained by departure of the (protonated) OH leaving group from a pseudoaxial position. The difference in stability of the carbocations is suggested to stem (a) from the greater hyperconjugative ability of a C-H than a C-OH bond and (b) from enhanced conjugation arising from the stabilizing influence of an aromatic ring in the no-bond resonance structures representing the hyperconjugation (C(6)H(6)OH(+) ? C(6)H(5)OH H(+)). This is consistent with an earlier suggestion by Mulliken and a demonstration by Schleyer that the benzenium ion is subject to hyperconjugative aromatic stabilization. It is proposed that, in analogy with the terms homoconjugation and homoaromaticity, arenium ions should be considered as "hyperaromatic".     

Amino-acid-dependent shift in tRNA synthetase editing mechanisms

Many aminoacyl-tRNA synthetases prevent mistranslation by relying upon proofreading activities at multiple stages of the aminoacylation reaction. In leucyl-tRNA synthetase (LeuRS), editing activities that precede or are subsequent to tRNA charging have been identified. Although both are operational, either the pre- or post-transfer editing activity can predominate. Yeast cytoplasmic LeuRS (ycLeuRS) misactivates structurally similar noncognate amino acids including isoleucine and methionine. We show that ycLeuRS has a robust post-transfer editing activity that efficiently clears tRNA(Leu) mischarged with isoleucine. In comparison, the enzyme's post-transfer hydrolytic activity against tRNA(Leu) mischarged with methionine is weak. Rather, methionyl-adenylate is cleared robustly via an enzyme-mediated pre-transfer editing activity. We hypothesize that, similar to E. coli LeuRS, ycLeuRS has coexisting functional pre- and post-transfer editing activities. In the case of ycLeuRS, a shift between the two editing pathways is triggered by the identity of the noncognate amino acid.     

Examining the mechanism of action of a kinesin inhibitor using stable isotope labeled inhibitors for cross-linking (SILIC)

It is difficult to determine a chemical inhibitor's binding site in multiprotein mixtures, particularly when high-resolution structural studies are not straightforward. Building upon previous research involving photo-cross-linking and the use of mixtures of stable isotopes, we report a method, Stable Isotope Labeled Inhibitors for Cross-linking (SILIC), for mapping a small molecule inhibitor's binding site in its target protein. In SILIC, structure-activity relationship data is used to design inhibitor analogues that incorporate a photo-cross-linking group along with either natural or 'heavy' stable isotopes. An equimolar mixture of these inhibitor analogues is cross-linked to the target protein to yield a robust signature for identifying inhibitor-modified peptide fragments in complex mass spectrometry data. As a proof of concept, we applied this approach to an ATP-competitive inhibitor of kinesin-5, a widely conserved motor protein required for cell division and an anticancer drug target. This analysis, along with mutagenesis studies, suggests that the inhibitor binds at an allosteric site in the motor protein.     

Hydrogen-bonded inclusion compounds with reversed polarity: anionic metal-complexes and cationic organic linkers

Synthesized and structurally characterized is a new series of soft-host frameworks assembled by charge-assisted hydrogen bonds between an anionic metal complex (MC) and cationic organic linkers (OL), specifically [Co(en)(ox)(2)](-) and diprotonated 4,4'-bipyridinium (H(2)bpy) or 1,2-bis(4-pyridinium)ethylene (H(2)bpye). While frameworks built of cationic complexes and anionic organic linkers are already well-known, the seven new compounds described here represent the first series of frameworks with reversed polarity, that is, made of anionic complexes and cationic organic linkers. The compounds have a general formula [OL][MC](2)·n(guest), where the guest molecules 4,4'-biphenol (bp), 4-methoxyphenol (mp), 1,4-dimethoxybenzene (dmb), 1,6-dimethoxynaphtalene (dmn), and 4-nitroanisole (na). Structurally the compounds can be described as pillared-layer frameworks with layers constructed of MC anions and linked together by hydrogen-bonded cationic OL pillars. The guest molecules occupy the galleries between the pillars while their steric, electronic, and π-π and hydrogen-bonding capabilities influence the overall structure of the soft frameworks.     

Acid-catalyzed dehydration of naphthalene-cis-1,2-dihydrodiols: origin of impaired resonance effect of 3-substituents

Acid-catalyzed dehydrations of substituted naphthalene-cis-1,2-dihydrodiols occur with loss of the 1- or 2-OH group to form 2- and 1-naphthols, respectively. Effects of substituents MeO, Me, H, F, Br, I, and CN at 3-, 6-, and 7-positions of the naphthalene ring are consistent with rate-determining formation of β-hydroxynaphthalenium ion (carbocation) intermediates. For reaction of the 1-hydroxyl group the 3-substituents are correlated by the Yukawa-Tsuno relationship with ρ = -4.7 and r = 0.25 or by σ(p) constants with ρ = -4.25; for reaction of the 2-hydroxyl group the 3-substituents are correlated by σ(m) constants with ρ = -8.1. The correlations for the 1-hydroxyl imply a surprisingly weak resonance interaction of +M substituents (MeO, Me) with a carbocation reaction center but are consistent with the corresponding correlation for acid-catalyzed dehydration of 3-substituted benzene-cis-1,2-dihydrodiols for which ρ = -6.9 and r = 0.43. Substituents at the 6- and 7-positions of the naphthalene rings by contrast are correlated by σ(+) with ρ = -3.2 for reaction of the 1-hydroxyl group and ρ = -2.7 for reaction of the 2-hydroxyl group. The unimpaired resonance implied by these substituent effects appears to be inconsistent with a previous explanation of the weak resonance of the 3-substituents in terms of imbalance of charge development and/or nonplanarity of the benzenium ring in the transition state. An alternative possibility is that the adjacent hydroxyl group interferes sterically with conjugation of +M substituents. "Hyperaromaticity" of the arenium ion intermediates does not appear to be a factor influencing this behavior.     

Enantioselective synthesis of all-carbon quaternary stereogenic centers in acyclic systems

Most of the methods for the creation of all-carbon quaternary stereogenic centers in acyclic systems were developed in the last decade showing the contemporary interest of this field of research. Initial strategies, where chiral entities were linked to carbon skeleton, to enantioselective catalysis and finally to strategies where several carbon-carbon bonds were created in a single-pot operation, reflect the constant strive and creativity in the design and execution of synthetic sequences. This feature article summarizes these sequences and is divided into sections on substitution and additions reactions, alkylation, aldol, Mannich and rearrangements reactions. It is safe to predict that this field of chemistry will continue to grow exponentially in the coming decades and the ready availability of a wide range of these chiral entities will provide an excellent opportunity to further enrich mainstream synthetic methodologies.     

Sub-barrier fission fragment angular distributions for the system19F+232Th

The measurements of fission fragment angular distributions for the system¹⁹F+²³²Th have been extended to the sub-barrier energies of 89.3, 91.5 and 93.6 MeV. The measured anisotropies, within errors are nearly the same over this energy region. However, the deviation of the experimental values of anisotropies from that of standard statistical model predictions increases as the bombarding energy is lowered.     

Theoretical expression for change of extraordinary refractive index in annealed proton exchanged LiNbO3 optical waveguides

A general expression for the change in extraordinary refractive index of the annealed proton exchanged LiNbO₃ waveguide has been deduced. The expression deduced explains the experimental results of decrease in change of extraordinary refractive index with annealing. The effect of annealing time has also been incorporated following Cao's model (Cao, Ramaswamy, Srivastava, J. Lightwave Technol. 10 (1992) 1302–1313). The concentration profile of protons in the annealed waveguide has been deduced theoretically, which is consistent with the previous results. The spontaneous polarization has been considered as the central mechanism for change in extraordinary refractive index due to proton exchange with annealing.     

The transition from bulk to nano as a phase transition

It is demonstrated that the chemical potential of bosons trapped in a harmonic potential shows a discontinuity as a function of the number of particles in the system. In the model used, it is shown that if the number of particles is of the order of 10⁶ or greater, bulk-like behaviour is exhibited by the system. This translates to a ratio of V/V_c>10⁶ for bulk behaviour, where V is the crystallite volume of the experimental sample and V_c is the volume of the unit cell. Several experimental results covering a wide range of physical phenomena that corroborate the fact that such a number-induced phase transition indeed exists are presented.