Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation.

Despite the clinical ubiquity of anesthesia, the molecular basis of anesthetic action is poorly understood. Amongst the many molecular targets proposed to contribute to anesthetic effects, the voltage gated sodium channels (VGSCs) should also be considered relevant, as they have been shown to be sensitive to all general anesthetics tested thus far. However, binding sites for VGSCs have not been identified. Moreover, the mechanism of inhibition is still largely unknown. The recently reported atomic structures of several members of the bacterial VGSC family offer the opportunity to shed light on the mechanism of action of anesthetics on these important ion channels. To this end, we have performed a molecular dynamics "flooding" simulation on a membrane-bound structural model of the archetypal bacterial VGSC, NaChBac in a closed pore conformation. This computation allowed us to identify binding sites and access pathways for the commonly used volatile general anesthetic, isoflurane. Three sites have been characterized with binding affinities in a physiologically relevant range. Interestingly, one of the most favorable sites is in the pore of the channel, suggesting that the binding sites of local and general anesthetics may overlap. Surprisingly, even though the activation gate of the channel is closed, and therefore the pore and the aqueous compartment at the intracellular side are disconnected, we observe binding of isoflurane in the central cavity. Several sampled association and dissociation events in the central cavity provide consistent support to the hypothesis that the "fenestrations" present in the membrane-embedded region of the channel act as the long-hypothesized hydrophobic drug access pathway.

Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel.

Computational methods and experimental data are used to provide structural models for NaChBac, the homo-tetrameric voltage-gated sodium channel from the bacterium Bacillus halodurans, with a closed and partially open pore domain. Molecular dynamic (MD) simulations on membrane-bound homo-tetrameric NaChBac structures, each comprising six helical transmembrane segments (labeled S1 through S6), reveal that the shape of the lumen, which is defined by the bundle of four alpha-helical S6 segments, is modulated by hinge bending motions around the S6 glycine residues. Mutation of these glycine residues into proline and alanine affects, respectively, the structure and conformational flexibility of the S6 bundle. In the closed channel conformation, a cluster of stacked phenylalanine residues from the four S6 helices hinders diffusion of water molecules and Na(+) ions. Activation of the voltage sensor domains causes destabilization of the aforementioned cluster of phenylalanines, leading to a more open structure. The conformational change involving the phenylalanine cluster promotes a kink in S6, suggesting that channel gating likely results from the combined action of hinge-bending motions of the S6 bundle and concerted reorientation of the aromatic phenylalanine side-chains.

Molecular dynamics simulations of ionic liquid-vapour interfaces: effect of cation symmetry on structure at the interface.

The influence of alkyl chain symmetry of the imidazolium cation on the structure and properties of the ionic liquid-vapour interface has been addressed through molecular dynamics simulations. The anion chosen is bis(trifluoromethylsulfonyl)imide (NTf(2)). Profiles of number densities, orientation of cations, charge density, electrostatic potential, and surface tension have been obtained. At the interface, both cations and anions were present, and the alkyl chains of the former preferred to orient out into the vapour phase. A large fraction of cations preferred to be oriented with their ring-normal parallel to the surface and alkyl chains perpendicular to it. These orientational preferences are reduced in ionic liquids with symmetric cations. Although the charge densities at the interface were largely negative, an additional small positive charge density has been observed for systems with longer alkyl chains. The electrostatic potential difference developed between the liquid and the vapour phases were positive and decreased with increasing length of the alkyl group. The calculated surface tension of the liquids also decreased with increasing alkyl chain length, in agreement with experiment. The surface tension of an ionic liquid with symmetric cation was marginally higher than that of one with an asymmetric, isomeric cation.

Role of cation symmetry in intermolecular structure and dynamics of room temperature ionic liquids: simulation studies.

Molecular dynamics simulations of a series of bis(trifluoromethylsulfonyl)amide anion-based room temperature ionic liquids have been carried out to identify the effects of the molecular symmetry of the cation on the structure and dynamics of the liquid. Simulations of ionic liquids with imidazolium cation containing varying lengths of alkyl groups were performed. The calculated density and total X-ray scattering function of the liquids agree well with experimental data. Liquids containing symmetric cations ([C(n)C(n)im][NTf(2)]) are found to be more structured than those with asymmetric ones ([C(n)C(1)im][NTf(2)]), manifested in greater intermolecular ordering and slower dynamics.

Aqueous solution of [bmim][PF6]: ion and solvent effects on structure and dynamics.

A dilute aqueous solution of the salt 1-n-butyl,3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]) has been studied using molecular dynamics simulations to investigate the effect of ions on water and vice versa. The anion is found to diffuse faster than the cation in the solution, in contrast to observations in the pure ionic liquid. Distributions of pair energies have been employed to identify ion association, and around 13% of the ions were found to exist as pairs. The mean potential energy of water molecules present in the coordination shell of an anion is less than that of water molecules coordinated to a cation. The former kind also exhibit two distinct orientational preferences with respect to the anion. The larger diffusion coefficient of the anion is related to the faster dynamics of water molecules in its hydration layer, as evidenced from the relaxation of their residence time correlation function.

Intermolecular correlations in an ionic liquid under shear.

The behavior of a model room temperature ionic liquid under shear is explored using non-equilibrium molecular dynamics simulations. The external field reduces intermolecular structure in the liquid. However, orientational ordering of the molecules in the form of a nematic phase is observed under shear.

Ultrastructural, immunochemical, and cytochemical study of myeloperoxidase in myeloid leukemia HL-60 cells following treatment with succinylacetone, an inhibitor of heme biosynthesis.

Myeloperoxidase (MPO) is a heme-containing glycoprotein found in the primary granules (or azurophilic granules) of human polymorphonuclear leukocytes. In the present study, cultured myeloid leukemia HL-60 cells were exposed for 0-72 h to 250 microM 4,6-dioxoheptanoic acid (succinylacetone, SA), a specific inhibitor of heme biosynthesis, and the effects were evaluated using ultrastructural, immunochemical, and cytochemical methods. En bloc peroxidase staining of glutaraldehyde-fixed cells was accomplished with a 30-min exposure to 3,3'-diaminobenzidine (DAB) tetrahydrochloride. Ultrastructural examination revealed that peroxidase reactivity in the endoplasmic reticulum (ER) was relatively unchanged for 8 h and decreased between 12 and 24 h; however, ER lacked DAB-reactive peroxidase at 48-72 h. Peroxidase reactivity in the ER reappeared within 4 h after removal of SA. Seventy-two hours after exposure to SA the number of condensed cytoplasmic granules stained with DAB was significantly decreased, and many of the granules had a "target" appearance with a central DAB-reactive dense core. Staining of mitochondria was observed with overnight exposure to DAB and persisted in HL-60 cells treated 72 h with SA. Mitochondrial and nuclear morphology appeared unaltered. Immunostaining of MPO in thin sections of paraformaldehyde/glutaraldehyde-fixed unosmicated HL-60 cells, embedded in Lowicryl K4M, was accomplished with sequential exposure to an affinity-purified monospecific rabbit antibody to HL-60-MPO and protein A conjugated to 5- or 10-nm colloidal gold. Compared to untreated control HL-60 cells, cells exposed to SA for 48 h exhibited comparable to increased immunoreactive MPO in the ER, despite the absence of heme-dependent peroxidase reactivity. The data indicate that SA inhibits formation of enzymatically active MPO and that in the presence of SA, the ER contains a form(s) of MPO that lacks enzymatic reactivity.

Demethylation of specific sites in the 5'-flanking region of the CYP17 genes when bovine adrenocortical cells are placed in culture.

DNA methylation of CYP17 (steroid 17 alpha-hydroxylase) was studied in bovine adrenocortical cells, which lose the capacity to express this tissue-specific gene in culture by phenotypic switching. Restriction enzyme digestions, and sequencing of a lambda clone of a second CYP17 gene (CYP17A2), showed that there are at least three CYP17 genes in the bovine genome. Southern blotting of DNA digested with Msp I or Hpa II together with Eco RI was used to investigate the methylation status of Hpa II sites at -1.0 kb (H1), -1.8 kb (H2), and -2.3 kb (H4) in CYP17A1 and CYP17A2 and at -0.7 kb (H0) in CYP17A3. In cells and tissues other than white blood cells, H0 was nonmethylated whereas H1 was always methylated; H2 and H4 showed variation in methylation status among different cells and tissues. In particular, whereas H4 was methylated in the bovine adrenal cortex in vivo, there was a rapid and complete demethylation at H4 when adrenocortical cells were placed in culture. Sites downstream from H4 did not change methylation over the first six passages in culture; additionally, the coding region of CYP17 remained fully methylated under all conditions. In contrast to adrenocortical cells, DNA from fibroblasts was nonmethylated at H2, whereas all downstream sites were fully methylated. Digestion with another methylation-sensitive enzyme, Bsa HI, which has a site between H2 and H4, showed that this region is methylated in intact adrenal cortex but nonmethylated both in cultured adrenocortical cells and in fibroblasts. The specific changes in methylation at this site and at H4 in adrenocortical cells indicate a reproducible, environmentally determined change in methylation in adrenocortical cells when they are placed in culture.

Changes in gene expression during senescence of adrenocortical cells in culture.

Bovine adrenocortical cells undergo a process in which expression of steroid hydroxylases is lost progressively as a function of population doubling level (PDL) in culture. Each cytochrome P450 shows a characteristic rate of loss of expression as a function of PDL (in order of rates of loss: CYP11B >CYP21 >CYP17 >CYP11A). CYP11B and CYP21 require insulin-like growth factor I as well as cyclic AMP; these are the only factors required for induction in the primary culture. Middle- and later passage cells do not express CYP11B and CYP21 under the same conditions, but will do so when cells are grown in extracellular matrix Matrigel. In late-passage cells neither CYP17, CYP21, nor CYP11B are expressed, even in the presence of Matrigel; only CYP11A is expressed in late-passage cultures. When the different environmental factors required for induction of CYP11B and CYP21 are taken into account, induction of these genes disappears with the same kinetics as previously shown for CYP17 as a function of PDL. The primary cause of the loss of expression of these genes is likely to be a phenotypic switching event similar to that previously demonstrated for CYP17 by in situ hybridization. The mechanism of phenotypic switching is unknown. However, one HpaII site at -2.3 kb of CYP17 was methylated in the bovine adrenal cortex in vivo but showed rapid and complete demethylation when adrenocortical cells were placed in culture. This indicates a unique, reproducible, environmentally determined change in methylation, with as yet undetermined consequences. However, data from reporter constructs suggest that phenotypic switching does not result from a simple loss of regulatory factors that act within 2.5 kb of the promoter. Previous data suggested that SV40 T antigen may affect phenotypic switching, and thus that SV40 may be useful for the derivation of functional adrenocortical cell lines. Adaptation of methods previously used for bovine cells to human adrenocortical cells to produce SV40 T antigen-transfected clones yielded data indicating preservation of essential aspects of the human adrenocortical cell differentiated phenotype.

Changes in gene expression and DNA methylation in adrenocortical cells senescing in culture.

Recent experiments in cultured bovine adrenocortical cells show that the previously observed phenotypic switching of CYP17 (steroid 17 alpha-hydroxylase) expression is preceded at a much earlier time by changes in methylation in the CYP17 5' flanking region. Two CpG sites that are methylated in the adrenal cortex in vivo were observed to undergo rapid demethylation when adrenocortical cells were placed in culture. Two adjacent CpG sites that are also methylated in vivo did not demethylate; these two sites are completely nonmethylated in fibroblasts. All CpG sites downstream, in the promoter or coding region, are always methylated in all tissues and in bovine adrenocortical cells even after many population doublings in culture. In contrast to the specific and rapid demethylation of sites in CYP17, satellite I shows a slower and apparently random loss of methylation that extends over the entire replicative life span. These changes in methylation provide examples of genetic instability in cells that undergo senescence in culture. Future experiments will focus on the relationship of these events to the phenotypic switching process.

Purification and properties of 4-hydroxyphenylacetic acid 3-hydroxylase from Pseudomonas putida.

4-Hydroxyphenylacetic acid 3-hydroxylase is a key enzyme in the pathway for the microbial degradation of phenylalanine, tyrosine and many aromatic amines. This enzyme was purified to homogeneity from Pseudomonas putida by affinity chromatography. The protein had a molecular weight of 91,000 and was a dimer of identical subunits. It was a typical external flavoprotein monooxygenase and showed an absolute requirement of NADH for activity. The enzyme had a pH optimum of 7.5 and the Km values for 4-hydroxyphenylacetic acid and NADH were 2 x 10(-4) M and 5.9 x 10(-5) M respectively. It was strongly inhibited by heavy metal ions and thiol reagents, suggesting the possible involvement of -SH group(s) in enzyme reaction.