<i>In Silico</i> Investigation on KAR Signaling Reveals the Significant Dynamic Change of Its Receptor’s Structure

Karrikins (KARs) have been identified as a class of smoke-derived plant growth regulators widely functioning among angiosperms. However, little is known about the mechanism by which these molecules trigger the relevant signal transduction. In this research, conventional molecular dynamics simulations were used to investigate the dynamical behavior of the apo- and holo-forms of the KAR receptor KAI2. The results show that the dynamic binding conformation of KAR1 in the active site is not completely consistent with that in the static crystal and is largely affected by the residue segment of the receptor, Tyr150–Asn180. The binding of the ligand with KAI2 changes the distribution of the electrostatic potential near the active site and drives the conformational transition of the Tyr150–Asn180 segment with strong internal positive correlation. A “dual induction” signaling mechanism is proposed in view of the present calculations. Our work paves way for in-depth understanding of the KAR signal transduction mechanism and sheds light on further experimental and theoretical exploration

Insight into the Dynamic Interaction of Different Carbohydrates with Human Surfactant Protein D: Molecular Dynamics Simulations

The unbinding process of three monosaccharides―galactose, glucose, and mannose―from human surfactant protein D (hSP-D) was investigated by the molecular docking and molecular dynamics methods to explore the cause of different dynamic interaction between these monosaccharides and the protein. The results show that the low affinity of galactose for hSP-D is attributed to the different binding conformation from the other two monosaccharides. The sugar coordinates to the calcium ion by the hydroxyl groups in the C2 and C3 atoms, so it cannot form the effective interaction with hSP-D. Glucose and mannose have similar binding conformations with hSP-D. Their difference in the affinity is induced by the interaction between the hydroxyl group in the C2 atom and the residue Asp325. The direction of the hydroxyl group in mannose results in the formation of the hydrogen bond with Asp325 and further makes mannose hydrogen-bond to the residues Glu329 and Arg343 by the hydroxyl groups in the C3, C4, and C6 atoms. As glucose only forms three hydrogen bonds with the residues Glu321, Asn323, and Glu329 by the hydroxyl groups in the C3 and C4 atoms, its interaction with hSP-D is weaker than that of mannose. Thus glucose has a lower energy barrier of dissociation. This work could provide the more penetrating understanding of hSP-D physiological functions

Dearomatization of Benzenoid Arenes Triggered by Triplet Excited State Intramolecular Proton Transfer

The detailed mechanism of photoinduced dearomatization of benzenoid arenes is investigated using both the high-level ab initio method and density functional theory. The results suggest that the optically allowed singlet excited state (S2) can quickly decay to the lowest triplet excited state (T1) through a barrierless internal conversion and intersystem crossing. Importantly, we find a triplet excited state intramolecular proton transfer (T-ESIPT) pathway to produce a diradical triplet intermediate (3MO–H), which can trigger the subsequent [4 + 2] dearomatization reaction. Furthermore, the diastereoselectivity of the reaction was illustrated by the rotation of the O–H group of 3MO–H, which could be effectively modulated by the solvent effect (arising from the strength of the intermolecular hydrogen bond) and the substituted effect (arising from the strength of the electron-donation group). This photochemical mechanism can explain well the experimental observations, and the novel T-ESIPT process can open a new door in studying the photoinduced proton transfer reactions

Phenotypes of each line in the presence of mannitol treatment during seed germination and early growth.

(A) Mannitol sensitivity of all lines at the germination stage. Surface-sterilized seeds were sown on MS medium supplemented with 0, 100, 200, or 300 mM mannitol, and incubated at 22°C for 7 d under a 16-h light and 8-h dark photoperiod. (B) Quantification of radicle emergence at 3 d after sowing and cotyledon greening at 7 d after sowing in response to mannitol. Data represent means ± SD from four biological replicates (n = 144).</p

Expression of stress/ABA-responsive genes in the wild-type and the <i>35S</i>:<i>TsApx6-GFP</i> plants subjected to salt stress.

Total RNA was purified from plants (4-week-old) treated with 300 mM NaCl for 6 h or 72 h and subjected to qPCR analysis. The expression of a gene in the WT grown under the control conditions was regarded as 1. The transcript abundance was normalized to the expression levels of Actin2 gene. Data represent means ± SD (n = 3) from three technical replicates. Asterisks indicate significant difference from the corresponding WT (*: P P < 0.01).</p

Root growth of all lines in response to different concentrations of NaCl or mannitol.

<p>Surface-sterilized seeds were germinated on full-strength MS medium for 3 d and the seedlings were then moved to fresh MS medium that contained 0, 50 or 100 mM NaCl or 100, 200 or 300 mM mannitol and grown vertically for 10 d. Bars = 0.5 cm. The data represent the means ± SD (n = 45). Means followed by different letters are significantly different at <i>P</i> < 0.05.</p

Phenotypes of each line in the presence of NaCl treatment during seed germination and early growth.

<p>(A) Sensitivity to NaCl in the WT, <i>atapx6</i>, and <i>TsApx6</i> transgenic plants during seed germination. Surface-sterilized seeds were sown on MS media contained 0, 50, 100 or 150 mM NaCl, and incubated at 22°C for 7 d under a 16-h light and 8-h dark photoperiod. Size bar = 0.5 cm. (B) Quantification of radicle appearance at 3 d after sowing and cotyledon greening at 7 d after sowing in response to NaCl. Data represent means ± SD from four biological replicates (n = 144).</p

Putative <i>cis</i>-elements present in the promoter sequence of <i>TsApx6</i>.

<p>Putative <i>cis</i>-elements present in the promoter sequence of <i>TsApx6</i>.</p

Histochemical staining and GUS assay of transgenic <i>Arabidopsis</i> lines Ts6P and Ts6P-M₀ in different tissues.

<p>(A) Histochemical staining of seedlings, leaves, flowers, stems and siliques. (B) GUS activities of the tissues from Ts6P and Ts6P-M₀ transgenic plants. A significant difference (<i>P</i> < 0.05) among the tissues is shown by different letters (a-f).</p

Expression of <i>TsApx6</i> and <i>AtApx6</i> under the salt stress conditions as revealed by qPCR analysis.

<p><i>Thellungiella</i> plants (six-week-old) and <i>Arabidopsis</i> plants (four-week-old) were treated with 300 mM NaCl for 0, 2, 4, 6, 8, 10, 12, 24, 36, or 48 h, respectively. Data are shown as the means ± standard deviation (SD) from three replicates.</p