Ab initio path‐integral calculations of kinetic and equilibrium isotope effects on base‐catalyzed RNA transphosphorylation models

Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self‐cleavage of RNA strands by 2′‐O‐transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2′‐O‐transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic‐structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold‐standard” coupled‐cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path‐integral method, that is, automated integration‐free path‐integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. © 2014 Wiley Periodicals, Inc.     

An extension of a theorem of Frobenius and Stickelberger to modules of projective dimension one over a factorial domain

Let R be a Cohen–Macaulay ring. A quasi-Gorenstein R-module is an R-module such that the grade of the module and the projective dimension of the module are equal and the canonical module of the module is isomorphic to the module itself. After discussing properties of finitely generated quasi-Gorenstein modules, it is shown that this definition allows for a characterization of diagonal matrices of maximal rank over a Cohen–Macaulay factorial domain R extending a theorem of Frobenius and Stickelberger to modules of projective dimension 1 over a commutative factorial Cohen–Macaulay domain.     

NUMERICAL METHODS FOR MISCIBLE DISPLACEMENT IN POROUS MEDIA INFLUENCED BY MOBILE WATER AND IMMOBILE WATER

1　ＩｎｔｒｏｄｕｃｔｉｏｎＩｎｒｅｃｅｎｔｙｅａｒｓ,ｔｈｅｉｎｔｅｎｔｉｏｎａｌｏｒａｃｃｉｄｅｎｔａｌｒｅｌｅａｓｅｏｆｔｈｅｃｈｅｍｉｃａｌｗａｓｔｅｓｏｎｓｏｉｌｓｈａｓｆｕｒｔｈｅｒｓｔｉｍｕｌａｔｅｄｃｕｒｒｅｎｔｉｎｔｅｒｅｓｔｓｉｎｔｈｅｍｏｖｅｍｅｎｔｏｆｃｈｅｍｉｃａｌｓ.Ｄｉｓｐｌａｃｅｍｅｎｔｓｔｕｄｉｅｓｈａｖｅｂｅｃｏｍｅｉｍｐｏｒｔａｎｔｔｏｏｌｓｉｎｓｏｉｌｐｈｙｓｉｃｓ,ｐａｒｔｉｃｕｌａｒｌｙｆｏｒｐｒｅｄｉｃｔｉｎｇｔｈｅｍｏｖｅｍｅｎｔｏｆｐｅｓｔｃｉｄｅｓ…     

A parallel multigrid algorithm for percolation clusters

A new parallel cluster-finding algorithm is formulated by using multigrid relaxation methods very similar to those used for differential equation solvers. For percolation clusters, this approach drastically reduces critical slowing down relative to local or scan relaxation methods. Numerical studies of scaling properties with system size are presented in the case of the 2D percolation clusters of the Swendsen-Wang Ising dynamics running on the Connection Machine.     

Observation of differential reactivity of cyclic amines in SN2 and SNAr displacement reactions in the course of synthesizing C-6, C-7 substituted quinolinecarbonitrile MEK1 kinase inhibitors

We have previously reported on a series of 4-anilino-6,7-dialkoxy-3-quinolinecarbonitriles as potent inhibitors of MEK1 kinase. Herein, we describe our synthetic efforts toward a series of 4-anilino-6-alkoxy-7-amino-3-quinolinecarbonitriles. In the course of this work, we were able to rapidly construct a library of 4-anilino-6-alkoxy-7-amino-3-quinolinecarbonitriles by simultaneous or sequential S_N2 (displacement) reactions on the C-6 chloroalkoxy moiety and S_NAr (addition/elimination) reactions at C-7 with nucleophilic amines.     

Exploration of structure--activity relationships among foldamer ligands for a specific protein binding site via parallel and split-and-mix library synthesis

We describe the use of parallel and split-and-mix library synthesis strategies for exploration of structure-activity relationships among peptidic foldamer ligands for the BH3-recognition cleft of the anti-apoptotic protein Bcl-xL. This effort began with a chimeric (alpha/beta+alpha)-peptide oligomer (composed of an alpha/beta-peptide segment and an alpha-peptide segment) that we previously identified to bind tightly to the target cleft on Bcl-xL. The side chains that interact with Bcl-xL were varied in a 1000-member one-bead-one-compound library. Fluorescence polarization (FP) screening identified four new analogues with binding affinities similar to that of the lead compound but no analogues with enhanced affinity. These results suggested that significant improvements in affinity were unlikely in this series. We then used library synthesis to examine backbone variations in the C-terminal alpha-peptide segment of the lead compound. These studies provided an opportunity for direct comparison of parallel and split-and-mix synthesis formats for foldamer libraries with respect to synthetic variability and assay sensitivity. We found that compounds from both the parallel and one-bead-one-compound libraries could be reliably screened in a competition FP assay without purification of library members. Our findings should facilitate the use of combinatorial library synthesis for exploration of foldamers as inhibitors of protein-protein interactions.     

Alcohol cosurfactants in hydrate antiagglomeration

Because of availability, as well as economical and environmental considerations, natural gas is projected to be the premium fuel of the 21st century. Natural gas production involves risk of the shut down of onshore and offshore operations because of blockage from hydrates formed from coproduced water and hydrate-forming species in natural gas. Industry practice has been usage of thermodynamic inhibitors such as alcohols often in significant amounts, which have undesirable environmental and safety impacts. Thermodynamic inhibitors affect bulk-phase properties and inhibit hydrate formation. An alternative is changing surface properties through usage of polymers and surfactants, effective at 0.5 to 3 weight % of coproduced water. One group of low dosage hydrate inhibitors (LDHI) are kinetic inhibitors, which affect nucleation rate and growth. A second group of LDHI are antiagglomerants, which prevent agglomeration of small hydrate crystallites. Despite great potential, work on hydrate antiagglomeration is very limited. This work centers on the effect of small amounts of alcohol cosurfactant in mixtures of two vastly different antiagglomerants. We use a model oil, water, and tetrahydrofuran as a hydrate-forming species. Results show that alcohol cosurfactants may help with antiagglomeration when traditional antiagglomerants alone are ineffective. Specifically, as low as 0.5 wt. % methanol cosurfactant used in this study is shown to be effective in antiagglomeration. Without the cosurfactant there will be agglomeration independent of the AA concentration. To our knowledge, this is the first report of alcohol cosurfactants in hydrate antiagglomerants. It is also shown that a rhamnolipid biosurfactant is effective down to only 0.5 wt. % in such mixtures, yet a quaternary ammonium chloride salt, i. e., quat, results in hydrate slurries down to 0.01 wt. %. However, biochemical surfactants are less toxic and biodegradable, and thus their use may prove beneficial even if at concentrations higher than chemical surfactants.     

Inherent antibacterial activity of a peptide-based beta-hairpin hydrogel

Among several important considerations for implantation of a biomaterial, a main concern is the introduction of infection. We have designed a hydrogel scaffold from the self-assembling peptide, MAX1, for tissue regeneration applications whose surface exhibits inherent antibacterial activity. In experiments where MAX1 gels are challenged with bacterial solutions ranging in concentrations from 2 x 10(3) colony forming units (CFUs)/dm2 to 2 x 10(9) CFUs/dm2, gel surfaces exhibit broad-spectrum antibacterial activity. Results show that the hydrogel surface is active against Gram-positive (Staphylococcus epidermidis, Staphylococcus aureus, and Streptococcus pyogenes) and Gram-negative (Klebsiella pneumoniae and Escherichia coli) bacteria, all prevalent in hospital settings. Live-dead assays employing laser scanning confocal microscopy show that bacteria are killed when they engage the surface. In addition, the surface of MAX1 hydrogels was shown to cause inner and outer membrane disruption in experiments that monitor the release of beta-galactosidase from the cytoplasm of lactose permease-deficient E. coli ML-35. These data suggest a mechanism of antibacterial action that involves membrane disruption that leads to cell death upon cellular contact with the gel surface. Although the hydrogel surface exhibits bactericidal activity, co-culture experiments indicate hydrogel surfaces show selective toxicity to bacterial versus mammalian cells. Additionally, gel surfaces are nonhemolytic toward human erythrocytes, which maintain healthy morphologies when in contact with the surface. These material attributes make MAX1 gels attractive candidates for use in tissue regeneration, even in nonsterile environments.     

Recent developments of bio-molecular motors as on-chip devices using single molecule techniques

The integration of microfluidic devices with single molecule motor detection techniques allows chip based devices to reach sensitivity levels previously unattainable.     

Reversible stiffening transition in beta-hairpin hydrogels induced by ion complexation

We have previously shown that properly designed lysine and valine-rich peptides undergo a random coil to beta-hairpin transition followed by intermolecular self-assembly into a fibrillar hydrogel network only after the peptide solutions are heated above the intramolecular folding transition temperature. Here we report that these hydrogels also undergo a stiffening transition as they are cooled below a critical temperature only when boric acid is used to buffer the peptide solution. This stiffening transition is characterized by rheology, dynamic light scattering, and small angle neutron scattering. Rheological measurements show that the stiffening transition causes an increase in the hydrogel storage modulus (G') by as much as 1 order of magnitude and is completely reversible on subsequently raising the temperature. Although this reversible transition exhibits rheological properties that are similar to polyol/borax solutions, the underlying mechanism does not involve hydroxyl-borate complexation. The stiffening transition is mainly caused by the interactions between lysine and boric acid/borate anion and is not driven by the changes in the secondary structure of the beta-hairpin peptide. Addition of glucose to boric acid and peptide solution disrupts the stiffening transition due to competitive glucose-borate complexation.