Time dependence of RMSDs of ATP in five systems versus simulation time in the five systems.

<p>(A) The triphophate moiety of ATP. (B) The dihedral O_α3-P_β-O_β3-P_γ. (C) The P_α and P_γ atoms of triphosphate moiety of ATP.</p

Time dependence of Cα atoms RMSDs of CDK9/cyclin T1 for five simulations in the 50 ns MD simulations.

<p>Systems 1, 2, 3, 4, and 5 are shown in black, red, blue, orange, and magenta, respectively. The same colors are maintained in the following Figs.</p

Schematic representation of the hydrogen bonds and coordination bonds in ATP active site in System 5 and in four CDK2 X-ray structures.

<p>(A) pCDK9/cyclin T1/ATP/2MG/Tat complex in System 5, (B) TS complex pCDK2/cyclinA/ADP/2MG/MgF₃^-/peptide (PDB code 3QHR) solved at pH 8.0, (C) TS complex pCDK2/cyclinA/ADP/2MG/MgF₃^-/peptide (PDB code 3QHW) solved at pH 8.25, (D) pCDK2/cyclinA/ADP/1MG complex (PDB code 4II5), (E) pCDK2/cyclinA/ADP/2MG complex (PDB code 4I3Z).</p

Hydrogen bonds and coordination bonds at the ATP binding pocket of CDK9 in five systems.

<p>CDK9 is shown as a gray ribbon with a gray stick representing residues involved in hydrogen bond or coordination bond. ATP is depicted by a yellow stick. All oxygen atoms, nitrogen atoms, and phosphate atoms are depicted in red, blue, and orange, respectively. Mg₁²⁺ and Mg₂²⁺ ions are exhibited as green spheres and water molecules are shown as red spheres. Red dotted lines indicate hydrogen bonds and blue dotted lines represent coordination bonds.</p

The compositions of the five simulations.

<p>The compositions of the five simulations.</p

DCCM for System 1 (A), System 2 (B), System 3 (C), System 4 (D), and System 5 (E).

<p>DCCM for System 1 (A), System 2 (B), System 3 (C), System 4 (D), and System 5 (E).</p

Effect of Biofilm on Passive Sampling of Dissolved Orthophosphate Using the Diffusive Gradients in Thin Films Technique

We evaluated the possibility of sampling dissolved orthophosphate using the diffusive gradient in thin films (DGT) technique with a phosphate ion-imprinted polymer (PIP)-based adsorbent and assessed the effect of biofilm on the DGT measurement. The composition of biofilm formed on the DGT surface was analyzed, and the effect of biofouling on the diffusion coefficient of the analyte was investigated. The corrected diffusion coefficient for the biofouled DGT was estimated and used for the calculation of the DGT equation. PIP-binding gels had a higher adsorption affinity for orthophosphate than for the other anions, indicating its selectivity for orthophosphate. The concentrations predicted via DGT agreed well with the concentrations determined in the bulk solutions. Sampling of orthophosphate using PIP-DGT was consistent over a pH range of 3–9 and ionic strength range of 0.01–10 000 μM. Other P compounds cannot be measured using the PIP-DGT technique. The diffusion coefficient of the orthophosphate linearly decreased with increasing thickness of the biofilm. This sampling method performed predictably in freshwater when the biofilm was not formed or when value for the biofilm interference was reduced by using the corrected diffusion coefficient

Superimposition of the CDK9 in snapshot at 50 ns in System 5 with those in the other four systems.

<p>(A) Superimposition of the CDK9 in System 1 (cyan) and System 5; (B) superimposition of the CDK9 in System 2 (magenta) and System 5; (C) superimposition of the CDK9 in System 3 (yellow) and System 5; (D) superimposition of the CDK9 in System 4 (orange) and System 5. The pCDK9/cyclin T1 is gray and HIV-1 Tat is red in System 5. The hydrogen bonds or salt bridges formed in System 5 are depicted by the red dotted line, and these interactions in other systems are described by the green dotted line.</p

Distances between phosphate group of pThr186 and guanidine group of arginine triad versus simulation time.

<p>The distance between pThr186 and Arg65 are shown in black and gray, the distance between pThr186 and Arg148 are shown in dark cyan and blue, and the distance between pThr186 and Arg172 are represented as red in System 2 (A), System 4 (B), and System 5 (C). The salt bridges in the pThr186 binding site at the 50 ns snapshot in three corresponding systems are shown in the right panel. Residues involved in salt bridge formation (red dotted line) are described by the stick with a red oxygen atom, blue nitrogen atom, and orange phosphorus atom.</p

Hydrogen Peroxide Electrosynthesis in a Strong Acidic Environment Using Cationic Surfactants

The two-electron oxygen reduction reaction (2e–-ORR) can be exploited for green production of hydrogen peroxide (H2O2), but it still suffers from low selectivity in an acidic electrolyte when using non-noble metal catalysts. Here, inspired by biology, we demonstrate a strategy that exploits the micellization of surfactant molecules to promote the H2O2 selectivity of a low-cost carbon black catalyst in strong acid electrolytes. The surfactants near the electrode surface increase the oxygen solubility and transportation, and they provide a shielding effect that displaces protons from the electric double layer (EDL). Compared with the case of a pure acidic electrolyte, we find that, when a small number of surfactant molecules were added to the acid, the H2O2 Faradaic efficiency (FE) was improved from 12% to 95% H2O2 under 200 mA cm–2, suggesting an 8-fold improvement. Our in situ surface enhanced Raman spectroscopy (SERS) and optical microscopy (OM) studies suggest that, while the added surfactant reduces the electrode’s hydrophobicity, its micelle formation could promote the O2 gas transport and its hydrophobic tail could displace local protons under applied negative potentials during catalysis, which are responsible for the improved H2O2 selectivity in strong acids