Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

Surface functionalization of polymer latex particles. II. Catalytic oxidation of poly(methylstyrene) latexes in the presence of cetyltrimethylammonium bromide

Surface-functionalized cationic poly(methylstyrene) (PMS) latex particles containing aldehyde and carboxylic acid groups were successfully achieved via an emulsion polymerization of 3(4)-methylstyrene in the presence of cetyltrimethylammonium bromide, followed by an in-situ oxidation catalyzed by copper chloride and tert-butyl hydroperoxide (t-BuOOH). Factors such as the type of metal catalyst, oxidant, and their concentration strongly affected the rate of oxidation. Step addition of t-BuOOH resulted in both a higher degree of oxidation and a more uniform distribution of particle size of the functionalized PMS as compared to the batch addition method. The effect of organic solvent was found to be insignificant, and the oxidation could still proceed in its absence. The particle sizes increased significantly during the oxidation but could be controlled by using crosslinked PMS latexes. Finally, the versatility of this oxidation process was demonstrated by oxidation of the polymer with a solid loading as high as 28%. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 3585–3593, 1997     

Designed helical peptides inhibit an intramembrane protease

gamma-Secretase cleaves the transmembrane domain of the amyloid precursor protein, a process implicated in the pathogenesis of Alzheimer's disease, and this enzyme is a founding member of an emerging class of intramembrane proteases. Modeling and mutagenesis suggest a helical conformation for the substrate transmembrane domain upon initial interaction with the protease. Moreover, biochemical evidence supports the presence of an initial docking site for substrate on gamma-secretase that is distinct from the active site, a property predicted to be generally true of intramembrane proteases. Here we show that short peptides designed to adopt a helical conformation in solution are inhibitors of gamma-secretase in both cells and enzyme preparations. Helical peptides with all d-amino acids are the most potent inhibitors and represent potential therapeutic leads. Subtle modifications that disrupt helicity also substantially reduce potency, suggesting that this conformation is critical for effective inhibition. Fluorescence lifetime imaging in intact cells demonstrates that helical peptides disrupt binding between substrate and protease, whereas an active site-directed inhibitor does not. These findings are consistent with helical peptides interacting with the initial substrate docking site of gamma-secretase, suggesting a general strategy for the development of potent and specific inhibitors of intramembrane proteases.     

Mycopyranone: A 8,8ˈ-binaphthopyranone with potent anti-MRSA activity from the fungus Phialemoniopsis sp.

A new 8,8?-binaphthopyranone (mycopyranone, 1) was isolated from a solid fermentation of Phialemoniopsis sp. (fungal strain MSX61662), and the structure was elucidated via analysis of the NMR and HRESIMS data. The axial chirality of 1 was determined to be M by ECD. The central chirality at C-4/C-4? was assigned through a modified Mosher’s method, while the absolute configuration at C-3/C-3? was deduced based on analysis of the ³J_H-3-H-4 values and NOESY correlations. Compound 1 was evaluated for its antimicrobial properties against Staphylococcus aureus SA1199 and a clinically relevant methicillin-resistant S. aureus strain (MRSA USA300 LAC strain AH1263). Compound 1 inhibited the growth of both strains in a concentration dependent manner with IC₅₀ values in the low μM range. Molecular docking indicated that compound 1 binds to the FtsZ (tubulin-like) protein in the same pocket as viriditoxin (2), suggesting that 1 targets bacterial cell division.     

Calculations of electron inelastic mean free paths. XII. Data for 42 inorganic compounds over the 50 eV to 200 keV range with the full Penn algorithm

We have calculated inelastic mean free paths (IMFPs) for 42 inorganic compounds (AgBr, AgCl, AgI, Al₂O₃, AlAs, AlN, AlSb, cubic BN, hexagonal BN, CdS, CdSe, CdTe, GaAs, GaN, GaP, GaSb, GaSe, InAs, InP, InSb, KBr, KCl, MgF₂, MgO, NaCl, NbC_0.712, NbC_0.844, NbC_0.93, PbS, PbSe, PbTe, SiC, SiO₂, SnTe, TiC_0.7, TiC_0.95, VC_0.76, VC_0.86, Y₃Al₅O₁₂, ZnS, ZnSe, and ZnTe) for electron energies from 50 eV to 200 keV. These calculations were made with energy-loss functions (ELFs) obtained from measured optical constants for 15 compounds while calculated ELFs were utilized for the other 27 compounds. Checks based on ELF sum rules showed that the calculated ELFs were superior to the measured ELFs that we had used previously. Our calculated IMFPs could be fitted to a modified form of the relativistic Bethe equation for inelastic scattering of electrons in matter for energies from 50 eV to 200 keV. The average root-mean-square (RMS) deviation in these fits was 0.60%. The IMFPs were also compared with a relativistic version of our predictive Tanuma-Powell-Penn (TPP-2M) equation. The average RMS deviation in these comparisons was 10.7% for energies between 50 eV and 200 keV. This average RMS deviation is almost the same as that found in a similar comparison for a group of 41 elemental solids (11.9%) although relatively large deviations were found for cubic BN (65.6%) and hexagonal BN (34.3%). If these two compounds are excluded in the comparisons, the average RMS deviation becomes 8.7%. We found generally satisfactory agreement between our calculated IMFPs and values from other calculations and from experiments.     

Protonation and bromination of an osmabenzyne: reactions leading to the formation of new metallabenzynes

The reactivities of benzynes and metal-carbyne complexes are normally associated with the triple bond units. However, we have now found that electrophiles do not attack the formal osmium-carbon triple bond of osmabenzyne complex 1. Instead, 1 undergoes electrophilic substitution reactions-the typical reactions of aromatic systems.     

Generation and Reactivity of a One-Electron-Oxidized Manganese(V) Imido Complex with a Tetraamido Macrocyclic Ligand

The synthesis and X-ray structure of a new manganese(V) mesitylimido complex with a tetraamido macrocyclic ligand (TAML), [Mn^V(TAML)(N-Mes)]⁻ ( 1 ), are reported. Compound 1 is oxidized by [(p-BrC₆H₄)₃N ]^+.[SbCl₆]⁻ and the resulting Mn^VI species readily undergoes H-atom transfer and nitrene transfer reactions.     

Direct aziridination of alkenes by a cationic (salen)ruthenium(VI) nitrido complex

[RuVI(N)(salchda)(CH3OH)]PF6 (1) (salchda = N,N'-bis(salicylidene)o-cyclohexyldiamine dianion) reacts readily with 2,3-dimethyl-2-butene at room temperature in the presence of pyridine or 1-methylimidazole to give initially [RuIV(Az1(-H))(salchda)(py)]PF6 (2, Az1 = 2,2,3,3-tetramethylaziridine), which is then slowly reduced to [RuIII(Az1)(salchda)(py)]PF6 (3). 1 also reacts with a variety of aryl-substituted alkenes such as styrene and trans-beta-methylstyrene in the presence of py or 1-MeIm to give the corresponding ruthenium(III) aziridine complexes. The structures of 3 and [RuIII(Az2)(salchda)(1-MeIm)]PF6 (4, Az2 = trans-2-methyl-3-phenylaziridine) have been determined by X-ray crystallography. The Ru-N(aziridine) distances (2.1049, 2.097 A) are consistent with a neutral aziridine ligand. The C-C and C-N distances in the aziridine ligands are all indicative of single bonds.     

Direct loading of polymer matrices in plastic microchips for rapid DNA analysis: A comparative study

We report the design and performance validation of microfluidic separation technologies for human identification using a disposable plastic device suitable for integration into an automated rapid DNA analysis system. A fabrication process for a 15-cm long hot-embossed plastic microfluidic devices with a smooth semielliptical cross section out of cyclic olefin copolymer is presented. We propose a mixed polymer solution of 95% w/v hydroxyethylcellulose and 5% w/v polyvinylpyrrolidone for a final polymer concentration of 2.5 or 3.0% to be used as coating and sieving matrix for DNA separation. This formulation allows preparing the microchip without pretreatment in a single-loading step and provides high-resolution separation (≈1.2 bp for fragments <200 bp), which is superior to existing commercial matrices under the same conditions. The hot-embossed device performance is characterized and compared to injection-molded devices made out of cyclic olefin copolymer based on their respective injector geometry, channel shape, and surface charges. Each device design is assessed by fluorescence videomicroscopy to evaluate the formation of injection plugs, then by comparing electropherograms for the separation of a DNA size standard relevant to human identification.