201 research outputs found
Sample Characteristics and Distribution of Smoking Duration among Male Ever Smokers Aged 18+, CHNS, 2006 (N = 2,637).
<p><sup>a</sup> nc refers to not being computed due to ties and/or insufficient uncensored cases.</p><p><sup>b</sup> Due to ties and/or insufficient uncensored cases, we can’t compute median durations of smoking for occupation and age group. To compare results, we estimated mean durations of smoking for occupation and age group, which tend to be lower than median durations of smoking.</p><p>Sample Characteristics and Distribution of Smoking Duration among Male Ever Smokers Aged 18+, CHNS, 2006 (N = 2,637).</p
Log-logistic Regression Models Estimating the Association between SES and Duration of Smoking among Male Ever Smokers Aged 18+, CHNS, 2006 (N = 2,637).
<p><sup>a</sup> Time ratios were computed by exponentiating the log-logistic regression coefficients.</p><p>*p<0.05, **p<0.01, ***p<0.001</p><p>Log-logistic Regression Models Estimating the Association between SES and Duration of Smoking among Male Ever Smokers Aged 18+, CHNS, 2006 (N = 2,637).</p
MD results for the WT enzyme (GLP).
<p>(A) A representative active-site structure along with the average values of some structural parameters of the reactant complex for the first methyl transfer. GLP is shown in balls and sticks, and AdoMet and the H3K9 sidechain are in sticks. Hydrogen atoms are not shown for clarity except for those on N<sub>ζ</sub> and transferable methyl group. Hydrogen bonds are indicated by red dotted lines, and the distances related to the reactant coordinate are also shown. (B) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions based on the 1.5-<i>ns</i> simulations of the reactant complex for the first methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (C) The active-site structure along with the average values of some structural parameters of the reactant complex for the second methyl transfer. (D) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the second methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (E) The structure of the reactant complex for the third methyl transfer. (F) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the third methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (G) A representative active-site structure along with the average values of some structural parameters near the transition state for the first methyl transfer obtained from the free energy (potential of mean force) simulations. (H) The structure along with the average values of some structural parameters near the transition state for the second methyl transfer. (I) The structure near the transition state for the third methyl transfer. All images were made by VMD <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037674#pone.0037674-HumphreyW1" target="_blank">[38]</a>. The distances shown on the structures are the calculated average distances from the trajectories over the 50-ps production runs in the corresponding window.</p
QM/MM free energy simulations of the reaction catalysed by (<i>4S</i>)-limonene synthase involving linalyl diphosphate (LPP) substrate
<p>A large number of terpenoid natural products are known to exist in nature. Terpene synthases are pivotal enzymes for the biosynthesis of diverse terpenoid skelotons. Monoterpene synthases are one type of terpene synthases responsible for the production of several hundreds of natural monoterpenes based on a very limited pool of substrates. Therefore, understanding detailed catalytic mechanisms of those enzymes are important for understanding the product specificity of terpene synthases. In this study, we present a detailed mechanistic description of the biosynthesis of the (<i>4S</i>)-α-terpinyl carbocation from (<i>3S</i>)-linalyl diphosphate (LPP) catalysed by (<i>4S</i>)-limonene synthase (LS) using two-dimensional QM/MM free energy (2D-PMF) simulations. Our estimated free energy barrier is in a reasonable agreement with the corresponding experimental kinetic data. We also perform the one-dimensional QM/MM free energy (1D-PMF) simulations and show that His579 can act as a general base to deprotonate (<i>4S</i>)-α-terpinyl carbocation and to generate the limonene product.</p
The definition of the structural parameters for monitoring the relative orientation of AdoMet and H3K9me1 [H3K9 and H3K9(me)<sub>2</sub>] in the reactant complex.
<p>The efficiency of the methyl transfer may be related to the distributions of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> in the reactant complexes. <i>θ</i> is defined as the angle between the two vectors <i>r</i><sub>1</sub> and <i>r</i><sub>2</sub>. Here <i>r</i><sub>1</sub> is the direction of the lone pair of electrons on N<sub>ζ</sub> and <i>r</i><sub>2</sub> is the vector pointing from C<sub>M</sub> to S<sub>δ</sub>. The reaction coordinate for calculating the free energy profiles for the methyl transfers is <i>R</i> = <i>r</i>(C<sub>M</sub>…S<sub>δ</sub>)−<i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>).</p
MD results for the Y1124F mutant.
<p>(A) A representative active-site structure along with the average values of some structural parameters of the reactant complex for the first methyl transfer. (B) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the first methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (C) The structure of the reactant complex for the second methyl transfer. (D) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the second methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (E) The structure of the reactant complex for the third methyl transfer. (F) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the third methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (G) A representative active-site structure along with the average values of some structural parameters near the transition state for the first methyl transfer. (H) The structure near the transition state for the second methyl transfer. (I) The structure near the transition state for the third methyl transfer.</p
MD results for the F1209Y mutant.
<p>(A) A representative active-site structure along with the average values of some structural parameters of the reactant complex for the first methyl transfer. (B) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the first methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (C) The structure of the reactant complex for the second methyl transfer. (D) Left: the two-dimensional plot of <i>r</i>(C<sub>M</sub>…N<sub>ζ</sub>) and <i>θ</i> distributions of the reactant complex for the second methyl transfer; Middle: the free-energy change as a function of <i>r</i>(C<sub>M</sub>…N<sub>ξ</sub>) obtained from the distributions; Right: the free-energy change as a function of <i>θ</i> obtained from the distributions. (E) The structure near the transition state for the first methyl transfer. (F) The structure near the transition state for the second methyl transfer.</p
Free energy profiles of methyl transfer processes in the Y1124F mutant.
<p>The first methyl transfer: blue and solid line with a free energy barrier of 13.9 kcal/mol; the second methyl transfer: red and dashed line with a free energy barrier of 15.9 kcal/mol; the third methyl transfer: green and dashed line with a free energy barrier of 13.3 kcal/mol.</p
Effect of <i>in vitro</i> Enhancer Deletion on <i>Cebpa</i> Expression and Myelopoiesis.
<p><b>A</b>) Mononuclear marrow cells from WT or Enh(f/f) mice were placed in IMDM/FBS with IL-3, IL-6 and SCF for 24 hr, transduced with pBabePuro (Puro) or pBabePuro-Cre (Cre) for 48 hr, puromycin selected for an additional 48 hr, and finally lineage-depleted. Genomic DNA was then subjected to PCR using the loxP5 or EnhΔ primer pairs followed by agarose gel electrophoresis and visualization by ethidium bromide staining. <b>B</b>) Total cellular RNAs were analyzed for <i>Cebpa</i> and large ribosomal subunit <i>mS16</i> mRNA expression. <i>Cebpa</i> RNA expression, normalized using <i>mS16</i> expression and set to 100 for WT marrow transduced with Cre, is shown (left, mean and SD from 3 determinations). Total cellular proteins isolated from the same groups of Lin<sup>-</sup> cells were subjected to Western blotting for C/EBPα and β-actin; locations of the p42 and p30 C/EBPα alternative translation variants are indicated (right). <b>C</b>) Lin<sup>-</sup> cells were placed in liquid culture with IMDM/FBS, IL-3, IL-6, and SCF and analyzed for surface CD11b and Gr-1 expression on day 4 (D4; mean and SD from three determinations). <b>D</b>) The morphology of Puro- or Cre-transduced Enh(f/f) cells from these cultures was assessed on D4 by Wright’s Giemsa staining; g—granulocyte; m—monocyte; b—blast. <b>E</b>) Lin<sup>-</sup> cells were cultured similarly in methylcellulose at 1E3 cell/mL, and myeloid CFUs were enumerated 7–8 days later (Gen1). CFU cells were then collected, washed with PBS, replated at 1E3 cells/mL, and analyzed similarly each 7 days (Gen 2 to Gen 12). In addition, a proportion of Gen5 cells were evaluated for their ability to proliferate in liquid culture in IMDM/FBS with IL-6/SCF or IL-3.</p
Model of cellobiohydrolase CelS structure in complex with celloheptaose (green), and cellobiose, colored in white (hydrogen), red (oxygen), and cyan (carbon).
<p>The sugar unit at subsite −1 was modelled manually. The substrate, celloheptaose, spans between subsites −1 to −7 in the substrate-binding tunnel, and cellobiose is bound in the cleft region between subsites +1 and +2. This figure was made using the VMD software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012947#pone.0012947-Humphrey1" target="_blank">[66]</a>.</p
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