Editor\u27s Notes, Chiba Medical Journal 90-1

Multiple sequence alignment of deduced amino acid sequences of 25 wheat annexin genes with rice annexin OsAnn2 (Os05g31760) obtained by ClustalW. (PDF 212 kb

Manipulation of Bowl-Shaped Nanoparticles Self-Assembled from a Bipyridine Pendant Containing Homopolymer

The morphological control and transformation of soft nanomaterials are critical for their physical and chemical properties, which can be achieved by dynamically regulating the hydrophilicity of amphiphilic polymers during self-assembly. Herein, an amphiphilic homopolymer poly(N-(2,2′-bipyridine)-4-acrylamide) (PBPyAA) with bipyridine pendants is synthesized, and the effect of various parameters including initial concentration, temperature, pH, and metal ion coordination on the self-assembly behavior and morphology of the assemblies is investigated. Upon changing the initial concentration of PBPyAA, bowl-shaped nanoparticles (BNPs) with precisely controlled diameter, opening size, and thickness are obtained. With the decrease of pH of the solution, the negatively charged surface of BNPs transforms to a positively charged state. Furthermore, the addition of divalent metal ions (Co2+, Mn2+, and Zn2+) induces the transformation of BNPs to vesicles and giant vesicles. The effect of the above factors on the morphology of the assemblies is essential to change the hydrophilicity of PBPyAA dynamically, leading to variation of the local viscosity during self-assembly. Overall, manipulation of the structural parameters of BNPs and transformation of BNPs to vesicles are achieved, providing fresh insights for the precise control of the morphologies of soft nanomaterials

Polymer/TiO₂ Hybrid Vesicles for Excellent UV Screening and Effective Encapsulation of Antioxidant Agents

Presented in this paper is a hybrid polymer/titanium dioxide (TiO₂) vesicle that has excellent UV-screening efficacy and strong capacity to encapsulate antioxidant agents. Poly­(ethylene oxide)-<i>block</i>-poly­(2-(dimethylamino)­ethyl methacrylate)-<i>block</i>-polystyrene (PEO-<i>b</i>-PDMAEMA-<i>b</i>-PS) triblock terpolymer was synthesized by atom transfer radical polymerization (ATRP) and then self-assembled into vesicles. Those vesicles showed excellent UV-screening property due to the scattering by vesicles and the absorption by PS vesicle membrane. The selective deposition of solvophobic tetrabutyl titanate in the PDMAEMA shell and the PS membrane of the vesicles led to the formation of polymer/TiO₂ hybrid vesicles, resulting in an enhanced UV-screening property by further reflecting and scattering UV radiation. The vesicles can effectively encapsulate antioxidant agents such as ferulic acid (up to 57%), showing a rapid antioxidant capability (within 1 min) and a long-lasting antioxidant effect

What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?

<div><p>Poliovirus (PV) is a well-characterized RNA virus, and the RNA-dependent RNA polymerase (RdRp) from PV (3D^pol) has been widely employed as an important model for understanding the structure-function relationships of RNA and DNA polymerases. Many experimental studies of the kinetics of nucleotide incorporation by RNA and DNA polymerases suggest that each nucleotide incorporation cycle basically consists of six sequential steps: (1) an incoming nucleotide binds to the polymerase-primer/template complex; (2) the ternary complex (nucleotide-polymerase-primer/template) undergoes a conformational change; (3) phosphoryl transfer occurs (the chemistry step); (4) a post-chemistry conformational change occurs; (5) pyrophosphate is released; (6) RNA or DNA translocation. Recently, the importance of structural motif D in nucleotide incorporation has been recognized, but the functions of motif D are less well explored so far. In this work, we used two computational techniques, molecular dynamics (MD) simulation and quantum mechanics (QM) method, to explore the roles of motif D in nucleotide incorporation catalyzed by PV 3D^pol. We discovered that the motif D, exhibiting high flexibility in either the presence or the absence of RNA primer/template, might facilitate the transportation of incoming nucleotide or outgoing pyrophosphate. We observed that the dynamic behavior of motif A, which should be essential to the polymerase function, was greatly affected by the motions of motif D. In the end, through QM calculations, we attempted to investigate the proton transfer in enzyme catalysis associated with a few amino acid residues of motifs F and D.</p> </div

Three truncated systems, including Lys167 (A), Lys359 (B) and Arg174 (C) separately, were used for quantum mechanics (QM) calculations.

<p>Each system contains the phosphate and sugar of the primer terminus adenosine nucleotide, Asp328, Asp233, crystal water, two Mg²⁺ ions, rCTP molecule.</p

B-factor values of the backbone alpha carbons for PV 3D^pol.

<p>(A) B-factor values of the backbone alpha carbons for PV 3D^pol in the apo and complex forms, which were obtained by averaging over five independent equilibrated MD trajectories. (B) B-factors of the backbone alpha carbons for PV 3D^pol in the apo form, which were obtained from MD simulation and crystallographic result. (C) B-factors of the backbone alpha carbons for PV 3D^pol in the complex form, which were obtained from MD simulation and crystallographic result. Please note that in the plots the crystallographic B-factors were shifted down in order to have clear comparison with MD derived values. The regions of the pinky finger and the thumb are indicated by the black boxes in the figures.</p

Accumulated contributions to the overall motion of PV 3D^pol.

<p>The results were obtained from five independent equilibrated MD trajectories. The results of PV 3D^pol in the apo and complex forms were plotted against the number of principal components, indicated by the black dash and solid lines respectively.</p

Alyssum campestre

<p>In the three states (I, II, III), the stick representations of CTP, Arg163, Lys167 and Arg174, are depicted in red, green and orange respectively, and the crystal structure is indicated in white gray.</p

The hydrogen bonding occupancy for the residue pairs between RNA and polymerase, which were calculated by averaging over five independent MD trajectories of PV 3D^pol in the complex form.

<p>The hydrogen bonding occupancy for the residue pairs between RNA and polymerase, which were calculated by averaging over five independent MD trajectories of PV 3D^pol in the complex form.</p

Free energy (in unit of kcal/mol) profiles of (A)

<p><b>(PC1, PC2) for PV 3D^pol in the apo form, (B)</b><b>(PC1, PC2) for PV 3D^pol in the complex form, (C)</b><b>(PC1, PC3) for PV 3D^pol in the apo form, (D)</b><b>(PC1, PC3) for PV 3D^pol in the complex form, (E)</b><b>(PC2, PC3) for PV 3D^pol in the apo form, (F)</b><b>(PC2, PC3) for PV 3D^pol in the complex form.</b> The first principal component (PC1) corresponds to the largest contribution, the second principal component (PC2) represents the next largest contribution to the overall motion of PV 3D^pol, and so on.</p