One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme

R67 dihydrofolate reductase (DHFR) is a novel enzyme that confers resistance to the antibiotic trimethoprim. The crystal structure of R67 DHFR displays a toroidal structure with a central active-site pore. This homotetrameric protein exhibits 222 symmetry, with only a few residues from each chain contributing to the active site, so related sites must be used to bind both substrate (dihydrofolate) and cofactor (NADPH) in the productive R67 DHFR?NADPH?dihydrofolate complex. Whereas the site of folate binding has been partially resolved crystallographically, an interesting question remains: how can the highly symmetrical active site also bind and orient NADPH for catalysis? To model this ternary complex, we employed DOCK and SLIDE, two methods for docking flexible ligands into proteins using quite different algorithms. The bound pteridine ring of folate (Fol I) from the crystal structure of R67 DHFR was used as the basis for docking the nicotinamide-ribose-P_i (NMN) moiety of NADPH. NMN was positioned by both DOCK and SLIDE on the opposite side of the pore from Fol I, where it interacts with Fol I at the pore's center. Numerous residues serve dual roles in binding. For example, Gln 67 from both the B and D subunits has several contacts with the pteridine ring, while the same residue from the A and C subunits has several contacts with the nicotinamide ring. The residues involved in dual roles are generally amphipathic, allowing them to make both hydrophobic and hydrophilic contacts with the ligands. The result is a `hot spot' binding surface allowing the same residues to co-optimize the binding of two ligands, and orient them for catalysis.     

A theoretical characterization of reactions of HOOO radical with guanine: formation of 8-oxoguanine

Hydrogen trioxide (HOOO) radical and other polyoxides of general formula, RO_nR (where R stands for hydrogen, other atoms or groups and n?≥?3), are believed to be key intermediates in atmospheric chemistry and biological oxidation reactions. In this contribution, DFT calculations using M06-2X density functional and the 6-31G(d,p) and 6-311+G(d,p) basis sets have been carried out to study different reactions of HOOO radical with guanine such as addition of HOOO radical at the C2, C4, C5, and C8 sites of guanine, abstraction of hydrogen atoms (H1, H2a, and H8) of guanine, and the mechanisms of oxidation of guanine with HOOO radical yielding 8-oxoguanine(a highly mutagenic derivative of guanine) and its radical in gas phase and aqueous media. The polarizable continuum model (PCM) has been used for solvation calculations in aqueous media. Our calculations reveal that the C8 site of guanine is the most reactive site for addition of HOOO radical, and adduct formed at this site would be appreciably stable. The rate constant (\( =\frac{K_bT}{h}{e}^{-\frac{\Delta {E}^b}{RT}} \)) at the C8 site is found to be 6.07?×?10⁷ (2.89?×?10⁷) s^?1 at the M06-2X/6-311+G(d,p) level of theory in gas phase (aqueous media). The calculated barrier energy and heat of formation of hydrogen abstraction reactions show that HOOO radical would not abstract hydrogen atoms of guanine. Oxidation of guanine with HOOO radical can occur following two schemes (Scheme 1 and Scheme 2). It is found that formation of 8-oxoguanine radical via Scheme 1 would predominate over formation of 8-oxoguanine via Scheme 2, in a reaction of HOOO radical and guanine. Thus, HOOO radical can be treated as a member of reactive oxygen species (ROS) which play key roles in biological oxidation reactions, in agreement with previous literature reports.     

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n,n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n‐mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11‐mer and 12‐mer were also studied. The geometry optimization calculations were performed at the RHF/6‐311G* level for all the cases and at the MP2/6‐311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6‐311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero‐point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory, the 6‐311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6‐311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6‐311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas‐phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 90–104, 2001     

A novel carbocatalytic hydride transfer strategy for efficient reduction of structurally different aldehydes and ketones in water

Reduced graphene oxide (rGO)–NaBH₄ is reported as mild and efficient catalyst-system for chemo-/regioselective reduction of structurally different aliphatic, aromatic as well as α,β-unsaturated aldehydes and ketones in water. The rGO was prepared by reducing graphene oxide using Tulsi leaf extract as bio-reductant. Operational simplicity, ambient reaction condition, high yield of pure products (80–97%), no by-product formation, no use of column chromatography for purification are the salient features of the envisaged protocol. Furthermore, the recovered TRGO was recycled and reused for subsequent reductions up to five times without any loss in activity.     

Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases

Tris(2-aminoethyl)amine derivatives with appended urea and sulfonamide groups are shown to facilitate the translocation of fluorescent phospholipid probes and endogenous phosphatidylserine across vesicle and erythrocyte cell membranes. The synthetic translocases appear to operate by binding to the phospholipid head groups and forming lipophilic supramolecular complexes which diffuse through the non-polar interior of the bilayer membrane.     

Observation of two diffusive relaxation modes in microemulsions by dynamic light scattering

Water-in-oil microemulsions stabilized by AOT and dispersed in n-alkane oils with a constant molar water-to-surfactant ratio were studied by dynamic light scattering. A dilution series (in the range of volume fraction of water plus surfactant, phi approximately 0.02-0.52) was used, which allowed us to extract information about droplet sizes, diffusion coefficients, interactions, and polydispersity from experimental data. We report the observation of two diffusive relaxation modes in a concentrated microemulsion (0.20 < phi < 0.5) due to density (collective diffusion) and concentration or polydispersity (self-diffusion) fluctuations. Below this concentration it was difficult to resolve two exponentials unambiguously, and in this case one apparent relaxation mode was observed. It was found that for a given composition self-diffusion is more pronounced in apparent relaxation mode for a shorter chain length alkane. The concentration dependence of these diffusion coefficients reflects the effect of hard sphere and the supplementary attractive interactions. It was observed that the attractive part becomes more pronounced in the case of a large alkane chain oil at a given temperature. This explains the shift of the region of microemulsion stability to lower temperatures for higher chain length alkanes. Increase in hydrodynamic radius, Rh, obtained from the diffusion coefficient extrapolated to infinite dilution was observed with increase of alkane chain length. The polydispersity in microemulsion systems is dynamic in origin. Results indicate that the time scale for local polydispersity fluctuations is at least 3 orders of magnitude longer than the estimated time between droplet collisions.     

Pd(II) inhibition during hexacyanoferrate(III) oxidation of sugars: A kinetic study

An inhibition effect of PdCl₂ on the rate of oxidation of sugars by alkaline hexacyanoferrate(III) has been observed. The order of reactions in hexacyanoferrate(III) and OH⁻ is zero and unity, respectively, while that in sugars decreases from unity at higher sugar concentration. The kinetic data and spectrophotometric evidence support the formation of {Pd^II − (sugar)} and {Pd^II − sugar)₂} complexes and their resistance to react with Fe(CN)₆³⁻ © 1996 John Wiley & Sons, Inc.     

Radical polymerization of styrene initiated by styrene–arsenic sulfide complex

Styrene forms a complex with arsenic sulfide which in DMF at 85°C initiates radical polymerization yielding high molecular weight polymer. The order of reaction, with respect to initiator and monomer, is 0.5 ± 0.02 and unity, respectively. The energy of activation for the system computed as 96 kJ mol^?1 and the polymerization is retarded by hydroquinone. A possible mechanism for reaction has also been proposed.     

Synthesis,characterization and catalytic activities of a reusable polymer-anchored palladium(II) complex: effective catalytic hydrogenation of various organic substrates

A poly(3,6-dibenzaldimino N-vinyl carbazole) Pd(II) complex has been synthesized and characterized by physicochemical and spectroscopic techniques. The complex was found to be highly active toward hydrogenation reactions of various organic substrates under atmospheric pressure at ambient temperature. A tentative reaction mechanism is proposed on the basis of kinetic studies and isolation of reactive intermediates. The catalyst shows good conversion rates, thermal stability and recyclability.