Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines

The docking problem faces two major challenges: the global optimization of a multivariable function, such as the energy, and the ability to discriminate between true and false positive results, i.e., native from nonnative structures based on the input energy function. Among all energy evaluation tools, only a local energy-minimization method using an accurate enough potential function is able to discriminate between native and nonnative structures. To meet these requirements, a Monte Carlo with energy-minimization method has been incorporated into a new ECEPP/3 docking program. The efficiency of the simulation results from the use of an energy-grid technique based on Bezier splines and from a simplification of the receptor by switching on the energy of only important residues of the active site. Simulations of a thrombin-inhibitor complex show that the global minimum of the energy function was reached in every independent run within less than 3 min of time on an IBM RX 6000 computer. For comparison, 10 standard independent Monte Carlo simulations with 10(6) steps in each were carried out. Only three of them led to a conformation close to the x-ray structure. The latter simulations required an average of 24 min and about 10 hr with and without the grid, respectively. Another important result is that the Bezier spline technique not only speeds up the calculation by reducing the number of operations during the energy evaluation but also helps in reaching the global minimum by smoothing out the potential energy surface.     

Exceptional convergent evolution in a virus

Replicate lineages of the bacteriophage phiX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.     

Energy Trapping in Dications

The energy interaction curves of a number of diatomic and polyatomic dication systems were calculated in order to study their energy-trapping properties. Generally, the ab initio complete active space multiconfiguration self-consistent field method was used in an extended valence + polarization basis set, with compact effective potentials replacing the core electrons. The diatomic dications include all ten possible binary combinations of oxygen, sulphur, selenium, and tellurium. O₂²⁺ shows the largest exothermicity, measured from equilibrium to the monocation combination asymptote, and highest barrier to dissociation. The calculated equilibrium bond length and harmonic vibrational frequency agree very well with experiment. The O₂²⁺, SO²⁺, SeO²⁺, and TeO²⁺ series show progressively decreasing exothermicities but similar barrier heights. The non-oxides, in contrast, show similar exothermicities but decreasing barriers with increasing size of the atom constituents. These trends are interpreted in terms of both valence bond curve-crossing and molecular orbital bonding models. The ozone dication, O₃²⁺, is found to have a number of low-lying singlet and triplet stationary state structures spanning near-linear to D_3h2+ symmetries. Although the calculated exothermicity is even larger than for O₂²⁺, the barrier to O₂⁺ + O⁺ dissociation is predicted to be low in each case. O₂²⁺ surrounded by six argon atoms to model an isolating environment shows increased equilibrium O–O bond length, decreased exothermicity, and increased barrier to dissociation, relative to the bare dication. O₂²⁺ flanked at each end by a perpendicularly oriented H₂ molecule in a staggered conformation is obstructed from direct conversion to the water dimer dication by a high barrier. However, [(H₂O)₂]²⁺ dissociates smoothly from equilibrium to two water monocations with a large exothermicity but a small barrier.     

Limited influence of the mesothelium on the influx of monocytes into the peritoneal cavity

Exposure of Farage, a human B-cell line, to interleukin 4 (IL4) reduced the amount of CD38 antigen on the surface of the cells and in cell lysates. No evidence was obtained for accelerated breakdown, shedding, or internalization of CD38 molecules following IL4 treatment, nor the accumulation of CD38 molecules in the cell interior. The inhibition of protein synthesis with cycloheximide (CXM) diminished the down-regulation of CD38 induced by IL4. CXM decreased the expression of CD38 in Farage cells with arrested mitosis, and IL4 failed to further reduce CD38 expression. Staurosporine, an inhibitor of serine/threonine protein kinases, and H7 (1-(5-isoquinolinylsulfonyl)-2-methylpiperazine), a preferential inhibitor of protein kinase C (PKC), abrogated the effect of IL4 on CD38, while inhibitors of other serine protein kinases W7 (N-(aminohexyl)-5-chloro-1-naphthalenesulfoamide) and H8 (N-(2-[methylamino]ethyl)-5-isoquinolinesulfonamide) failed to interfere with the effect of IL4. Phorbol 12-myristate 13-acetate (PMA), an activator of PKC, resembled IL4 in decreasing the expression of CD38, and either staurosporine or H7 abolished this effect. Genistein, an inhibitor of tyrosine kinases, increased the expression of CD38, but failed to abrogate the inhibitory effect of IL4 on CD38. It is concluded that serine/threonine protein kinases mediated the IL4-induced down-regulation of the expression of CD38 molecules in B cells.     

Expression and circular dichroism studies of the extracellular domain of the alpha subunit of the nicotinic acetylcholine receptor

To provide material suitable for structural studies of the nicotinic acetylcholine receptor, we have expressed and purified the NH2-terminal extracellular domain of the mouse muscle alpha subunit. Several constructs were initially investigated using Xenopus oocytes as a convenient small scale expression system. A fusion protein (alpha210GPI) consisting of the 210 NH2-terminal amino acids of the alpha subunit and a glycosylphosphatidylinositol anchorage sequence conferred surface alpha-bungarotoxin binding in oocytes. Coexpression of alpha210GPI with an analogous construct made from the delta subunit showed no evidence of heterodimer formation. The alpha210GPI protein was chosen for large scale expression in transfected Chinese hamster ovary cells. The alpha210GPI protein was cleaved from these cells and purified on an immunoaffinity column. Gel and column chromatography show that the purified protein is processed as expected and exists as a monomer. The purified protein also retains the two distinct, conformation-specific binding sites expected for the correctly folded alpha subunit. Circular dichroism studies of alpha210GPI suggest that this region of the receptor includes considerable beta-sheet secondary structure, with a small proportion of alpha-helix.     

Measurement of the elastic modulus of fibre-reinforced composites used as orthodontic wires

The mechanical properties of an orthodontic wire pultruded from S2-glass-reinforced polyethyleneterephthalate glycol (PETG) were measured using two experimental devices simulating clinical conditions. A comparison of moduli measured in the clinically relevant devices with those measured in a standard flexural test reveals that data obtained using small cross-section, short span length clinical specimens require corrections associated with clamping and shearing effects. The clamping effect dominates and is caused by the softening of the material near the clamps. The shear effect becomes important at high fibre volume fractions and small span/thickness ratios. With adoption of these corrections, good agreement between moduli calculated using rule of mixtures and those measured in clinical tests is achieved. The analytical base developed for prediction of the stiffness of the orthodontic wire for different span/thickness ratios improves the procedure for design of dental appliances.