Convergence Properties of Free-Energy Calculations - Alpha-Cyclodextrin Complexes as a Case-Study

By considering all possible mutations among four para-substituted phenols, p-chlorophenol, p-methylphenol, p-cyanophenol, and p-methoxyphenol, which bind as inclusion compounds in alpha-cyclodextrin, the convergence properties of thermodynamic integration free energy calculations using slow growth as compared to numerical quadrature are investigated and interpreted in terms of structural and dynamical properties of the molecular system. It is shown that a systematic increase in the calculated hysteresis can be expected with increasing simulation time in slow-growth calculations if the system is perturbed faster than the rate at which the various states that make up the equilibrium ensemble are sampled. Using numerical quadrature the effects of nonequilibrium can be largely separated from the effects of insufficient sampling. It is shown, however, that the apparent degree of convergence when using numerical quadrature does not necessarily reflect the accuracy of the calculation. The utility of formulating closed cycles in both the bound and unbound states as a means of determining the minimum error in a given calculation is demonstrated. The effects of the choice of pathway and of the choice of integration scheme on convergence within closed cycles are also discussed. Finally, the quality of the force field used and the relative importance of the force field as opposed to sampling considerations are assessed by comparing the estimated free energy differences to experimental data. It is shown that a meaningful appraisal of a specific force field cannot be made independent of sampling considerations. A modification to the GROMOS force field that improved the agreement between the calculated and experimental free energies for the mutation of p-chlorophenol to p-methylphenol is also proposed

Effects of oxatomide and derivatives on high affinity IgE receptor-activated signal transduction pathways in rat basophilic leukemia cells: Role of protein tyrosine hyperphosphorylation and inhibition of extracellular calcium influx

The antiallergic drug oxatomide and analogs inhibit mediator release from a rat basophilic leukemia (RBL-2H3) cell line, which is frequently used as a mast cell model. By investigating a series of derivatives of oxatomide with different inhibiting activities on exocytosis, we aimed to evaluate the role of their effects on the early steps of the signal transduction cascade in the inhibition of exocytosis. The active compounds induced hyperphosphorylation of tyrosine residues both in stimulated as well as in resting cells. Furthermore, some elevation of the inositol 1,4,5-trisphosphate (IP3) formation upon antigen activation was observed for the active derivatives. Ca2+ fluxes were also studied. The inhibition of the antigen-induced Ca-45(2+) influx correlated with the effects of the drugs on exocytosis. Furthermore, the inhibitory activity on antigen- and thapsigargin-mediated exocytosis correlated well. Adherence of the cells to fibronectin, stimulating cellular integrin receptors, was synergistic to antigen activation of the RBL cells. However, oxatomide did lack any effect on integrin-mediated processes, as the IC50 value for exocytosis was identical for fibronectin-adhered cells and standard cultured cells. We conclude that oxatomide and its analogs inhibit exocytosis, mainly by inhibiting Ca2+ influx over score operated Ca2+ (SOC) channels. The drugs have a direct effect on the store operated Ca2+ channels or affect the direct regulation of these channels. (C) 1998 Elsevier Science Inc

Predation on heterospecific larvae by adult females of Kampimodromus aberrans, Amblyseius andersoni, Typhlodromus pyri and Phytoseius finitimus (Acari: Phytoseiidae)

The predatory mites Kampimodromus aberrans (Oudemans), Amblyseius andersoni (Chant), Typhlodromus pyri Scheuten and Phytoseius finitimus Ribaga are important biological control agents in orchards and vineyards in Europe and elsewhere. They can coexist in the same habitat and engage in intraguild predation (IGP). In the laboratory we evaluated biological parameters of these predatory mites fed with heterospecific larvae considered as intraguild prey (IG-prey). Results suggest that A. andersoni should be considered the superior intraguild predator, while Phytoseius finitimus appeared to suffer from intraguild predation. The profiles of K. aberrans and T. pyri were less definite