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.     

Tracer diffusion of131I− ions in a few 1–2 electrolytes in agar gel

Tracer diffusion of¹³¹I^– ions is studied at different temperatures /20°C–50°C/ in 2.5% agar gel containing sodium and potassium sulphate solutions over a wide range of concentrations. The results are in qualitative agreement with the theoretical values in the concentration range 10^–6–10^–1M. Agar gel shows an obstruction effect to diffusional flow. The activation energy for tracer diffusion was found to be of the order of 16.3 kJ mol^–1.     

Structural analysis of underivatized sialic acids by combined high-performance liquid chromatography-mass spectrometry

Mass spectra of chemically ionized, positive ions of underivatized N,O-acylated sialic acids, 2-deoxy-2,3-didehydro-N-acetylneuraminic acid and sialyl-alpha(2-3)-lactose were obtained by combined high-performance liquid chromatography--mass spectrometry, using a direct liquid inlet system. The mass spectra of the different compounds for which fragmentation schemes are proposed enable the differentiation between sialic acids, although the localization of O-substituents is not possible. However, since the various sialic acids separated well on high-performance liquid chromatography, combined high-performance liquid chromatography-mass spectrometry allowed their unequivocal characterization.     

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.     

Complexes of Cobalt(II), Nickel(II) and Copper(II) Chloroacetates with Quinoline N-Oxide

Some 1:1 and 1:2 adducts of cobalt(II), nickel(II) and copper(II) chloroacetates with quinoline N -oxide have been isolated by the interaction of the appropriate metal chloroacetate with quinoline N -oxide (QuinNo). The complexes isolated are of 1:1 stoichiometry of formula (M(CH_3-xCl_xCOO)₂QuinNO) (when M=Co(II), Ni(Il); X=l, 2 and 3 and when M=Cu(II), X=1 and 2) except copper(II) trichloroacetate which yields an adduct of 1:2 stoichiometry of formula[Cu(CCl₃COO)₂ (QuinNO)₃]. The adducts isolated are soluble in common organic solvents.     

Study of Molecular Interactions in Binary Mixtures of Aniline with Carboxylic Acids at 293.15 K, 303.15 K and 313.15 K

Ultrasonic velocity, density, refractive index and viscosity of binary mixtures of aniline with acetic acid (AA) and propionic acid (PA) have been measured at 293.15, 303.15 and 313.15 K over the entire composition range. Further, the specific heat ratio, heat capacity, effective Debye temperature and pseudo-Gruensisen parameter and non-linearity parameter have been evaluated using ultrasonic absorption data. The deviation in isentropic compressibility, excess molar volume, excess intermolecular free length, deviation in molar refraction, deviation in viscosity, relaxation time, enthalpy, entropy and Gibbs energy of activation have been calculated from the experimental data and fitted with the Redlich-Kister polynomial equation. A comparative study has also been made between experimental and theoretically calculated values of densities using the HBT and Rackett density models. Mixing rules for the prediction of refractive index, e.g. Lorentz-Lorenz (L-L), Eykmen (Eyk), Weiner (W), Heller (H), Gladstone-Dale (G-D), Arago-Biot (A-B) and Newton (N) have been applied to these binary mixtures.