Binding of active site directed ligands to phospholipase A2: Implications on the molecular constraints and catalytic mechanism

Molecular constraints for the localization of active site directed ligands (competitive inhibitors and substrates) in the active site of phospholipase A2 (PLA2) are characterized. Structure activity relationships with known inhibitors suggest that the head : group interactions dominate the selectivity as well as a substantial part of the affinity. The ab initio fitting of the amide ligands in the active site was carried out to characterize the head group interactions. Based on a systematic coordinate space search, formamide is docked with known experimental constraints such as coordination of the carbonyl group to Ca2+ and hydrogen bond between amide nitrogen and ND1 of His48. An optimal position for a bound water molecule is identified and its significance for the catalytic mechanism is postulated. Unlike the traditional ''pseudo-triad'' mechanism, the ''Ca-coordinatedoxyanion'' mechanism proposed here invokes activation of the catalytic water to form the oxyanion in the coordination sphere of calcium. As it attacks the carbonyl carbon of the ester, a near-tetrahedral intermediate is formed. As the second proton of the catalytic water is abstracted by the ester oxygen, its reorientation and simultaneous cleavage form hydrogen bond with ND1 of His48. In this mechanism of esterolysis, a catalytic role for the water co-ordinated to Ca2+ is recognised.

Conjugate MHD flow past a flat plate

A boundary layer solution for the conjugate forced convection flow of an electrically conducting fluid over a semi-infinite flat plate in the presence of a transverse magnetic field is presented. The governing nonsimilar partial differential equations are solved numerically using the Keller box method. Values of the temperature profiles of the plate are obtained for various values of the parameters entering the problem and are given in a table and shown on graphs.

Construction of energy-level diagram of oriented benzene using connectivity information obtained by modified z-cosy experiment

Experiments involving selective perturbation of a transition yield information about the directly connected transitions, which in turn yield information for deriving the parameters of the spin Hamiltonian of oriented molecules. Problems involved with selective perturbation are removed by the use of a two-dimensional experiment, namely, the modified Z-COSY-experiment, The use of this experiment is demonstrated for obtaining the connectivity information and for determining the parameters of the spin Hamiltonian of oriented benzene, a strongly coupled six-spin system

Control of lipid microstructures by molecular design and its implications

An overview of the current trends in the lipid design for specific applications has been presented. Lipids with different surface charge and hydrophobic backbone undergo aggregation to produce lamellae or bilayer and multilayer vesicles in aqueous media. Various aspects of present development of chiral superstructures and enzyme-mimics have been discussed. Utility of these molecules for potential applications in immunomodulation and sustained drug-delivery systems is also summarized.

Multiscale Modeling Approach to Acoustic Emission during Plastic Deformation

We address the long-standing problem of the origin of acoustic emission commonly observed during plastic deformation. We propose a framework to deal with the widely separated time scales of collective dislocation dynamics and elastic degrees of freedom to explain the nature of acoustic emission observed during the Portevin-Le Chatelier effect. The Ananthakrishna model is used as it explains most generic features of the phenomenon. Our results show that while acoustic emission bursts correlated with stress drops are well separated for the type C serrations, these bursts merge to form nearly continuous acoustic signals with overriding bursts for the propagating type A bands.

Symmetry Properties of the Large-Deviation Function of the Velocity of a Self-Propelled Polar Particle

A geometrically polar granular rod confined in 2D geometry, subjected to a sinusoidal vertical oscillation, undergoes noisy self-propulsion in a direction determined by its polarity. When surrounded by a medium of crystalline spherical beads, it displays substantial negative fluctuations in its velocity. We find that the large-deviation function (LDF) for the normalized velocity is strongly non-Gaussian with a kink at zero velocity, and that the antisymmetric part of the LDF is linear, resembling the fluctuation relation known for entropy production, even when the velocity distribution is clearly non-Gaussian. We extract an analogue of the phase-space contraction rate and find that it compares well with an independent estimate based on the persistence of forward and reverse velocities.

Distribution of ionic charge carriers and migration barriers in binary alkali silicate glasses

Likely spatial distributions of network-modifying (and mobile) cations in (oxide) glasses are discussed here. At very low modifier concentrations, the ions form dipoles with non-bridging oxygen centres while, at higher levels of modification, the cations tend to order as a result of Coulombic interactions. Activation energies for cation migration are calculated, assuming that the ions occupy (face-sharing) octahedral sites. It is found that conductivity activation energy decreases markedly with increasing modifier content, in agreement with experiment.

Effect of the valine-threonine constraint on the dynamics of the proline helix — A molecular dynamics study

Proline residues in helices play an important role in the structure of proteins. The proline residue introduces a kink in the helix which varies from about 5-degrees to 50-degrees. The presence of other residues such as threonine or valine near the proline region can influence the flexibility exhibited by the kinked helix, which can have an important biological role. In the present paper, the constraint introduced by threonine and valine on a proline helix is investigated by molecular dynamics studies. The systems considered am (1) a poly-alanine helix with threonine-proline residues (TP) and (2) a poly-alanine helix with valine-threonine-proline residues (VTP), in the middle. Molecular dynamics simulations are carried out on these two systems for 500 ps. The results are analyzed in terms of structural transitions, bend-related parameters and sidechain orientations.

Factors contributing to phantom bonds in inorganic molecules: Interpretations and predictions

The validity of various qualitative proposals for interpreting and predicting the existence of short contacts between formally non-bonded atoms, as in cyclodisiloxane and related inorganic ring systems, is critically evaluated. The models range from simple considerations of geometric constraints, lone pair repulsions and pi-complex formation to proposals such as the unsupported pi-bond model and the sigma-bridged-pi bond concept. It is pointed out that a unified description based on a combination of closed and open 3-centre 2-electron bonds is possible. The role of hybridisation is emphasized in the short phantom bond computed in an earlier model system. These insights are used to predict structures with exceptionally short Si..Si and B..B phantom bonds. The proposals are confirmed by ab initio calculations.

Gibbs energy of formation of orthorhombic CaZrO3

The Gibbs free energy of formation of the orthorhombic form of CaZrO3(o) from monoclinic ZrO2(m) and periclase CaO(p) has been determined as a function of temperature in the range 950-1225 K, using an electrochemical cell incorporating single-crystal CaF2 as the solid electrolyte. The results are corrected for the small solid solubility of CaO in ZrO2. For the reaction, ZrO2(m) + CaO(p) --> CaZrO3(o), DELTAG(phi) = -31590 -13.9T(+/- 180) J mol-1. The ''second-law'' enthalpy of formation of CaZrO3 obtained from the results of this study at a mean temperature of 1090 K is in excellent agreement with the high-temperature solution calorimetric measurements of Muromachi and Navrotsky at 1068 K (J. Solid State Chem., 72 (1988) 244), and the average value of the bomb and acid solution calorimetric studies of Lvova and Feodosev (Zh. Fiz. Khim., 38 (1964) 28), Korneev et al. (Izv. Akad. Nauk SSSR, Neorg. Mater., 7 (1971) 886) and Brown and Bennington (Thermochim. Acta, 106 (1986) 183). The standard entropy of CaZrO3(o) at 298.15 K from the free energy data is 96.4 (+/- 3.5) J K-1 mol-1. The results of this study are discussed in comparison with high-temperture e.m.f. measurements reported in the literature on cubic zirconia solid solutions.

Investigation of exchange of energy between zeeman and dipolar reservoirs in the rotating frame in solids

Exchange of energy between Zeeman and dipolar reservoirs in the rotating frame during spin-lock has important implications for the understanding of the Hartmann-Hahn cross polarisation process and is examined here with experiments on ammonium dihydrogen phosphate. It is observed that energy exchange between the two reservoirs takes place indicating that the relative magnitude of the dipolar coupling in relation to the applied r.f. field may have a role to play in determining the rate of exchange of energy between the two reservoirs.

Ionic and dipolar solvation dynamics in liquid water

The solvation time correlation function for solvation in liquid water was measured recently. The solvation was found to be very fast, with a time constant equal to 55 fs. In this article we present theoretical studies on solvation dynamics of ionic and dipolar solutes in liquid water, based on the molecular hydrodynamic approach developed earlier. The molecular hydrodynamic theory can successfully predict the ultrafast dynamics of solvation in liquid water as observed from recent experiments. The present study also reveals some interesting aspects of dipolar solvation dynamics, which differs significantly from that of ionic solvation.