Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase

We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determining step is the release of the NH3 molecule.     

Novel molecularly hybridized polyethylene/silica composite materials: Polymerization of ethylene with supported titanocenes by mesoporous silicates

A novel molecularly hybridized polyethylene/silica composite thin film was obtained by the gas‐phase polymerization of ethylene with a titanocene‐mounted mesoporous silica layer on a mica plate with mesoscopic pores arranged on the film surface. However, the use of titanocene‐mounted hexagonal domains of mesoporous silica on a glass plate for the gas‐phase polymerization of ethylene resulted in the formation of an islanded polyethylene/silica hybridized material. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 4821–4825, 2000     

Electrostatic Assembly of Dendrimer Electrolytes: Negatively and Positively Charged Dendrimer Porphyrins

Carboxylate and ammonium functionalities—32 of each— facilitate electrostatic interaction between oppositely charged dendrimer electrolytes and porphyrin cores, which leads in protic media to a supramolecular, fluorescence-active aggregate of two chromophores that communicate and have a predictable topology (see drawing on the right; A=acceptor, D=donor). In contrast to the complexation of linear polyelectrolytes, the contact area for the two dendrimer molecules is very limited, just as one would expect for an assembly of spherical molecules.     

Lyophilised Platelet-Rich Fibrin: Physical and Biological Characterisation

Background: Platelet-rich fibrin (PRF) has gained popularity in craniofacial surgery, as it provides an excellent reservoir of autologous growth factors (GFs) that are essential for bone regeneration. However, the low elastic modulus, short-term clinical application, poor storage potential and limitations in emergency therapy use restrict its more widespread clinical application. This study fabricates lyophilised PRF (Ly-PRF), evaluates its physical and biological properties, and explores its application for craniofacial tissue engineering purposes. Material and methods: A lyophilisation method was applied, and the outcome was evaluated and compared with traditionally prepared PRF. We investigated how lyophilisation affected PRF’s physical characteristics and biological properties by determining: (1) the physical and morphological architecture of Ly-PRF using SEM, and (2) the kinetic release of PDGF-AB using ELISA. Results: Ly-PRF exhibited a dense and homogeneous interconnected 3D fibrin network. Moreover, clusters of morphologically consistent cells of platelets and leukocytes were apparent within Ly-PRF, along with evidence of PDGF-AB release in accordance with previously reports. Conclusions: The protocol established in this study for Ly-PRF preparation demonstrated versatility, and provides a biomaterial with growth factor release for potential use as a craniofacial bioscaffold.     

Sensing of chiral fullerenes by a cyclic host with an asymmetrically distorted pi-electronic component

Upon inclusion complexation with a racemic mixture of chiral fullerene C76 ((+/-)-C76), a novel cyclic host (1Rh) composed of a chiral N-methylporphyrin (PNMe) and a methylrhodium porphyrin (PRh) exhibited at 20 degrees C a 1H NMR spectral profile with diastereoisomerically split signals due to the NH group of PNMe. In contrast, because of a faster guest exchange dynamics, metal-free reference 12H, under identical conditions, did not show any signature of such diastereoisomeric splitting. Owing to the excellent resolution (15.6 Hz) of the split NH signals, the complexation with 1Rh allowed for the accurate determination of the optical purity of C76. On the basis of the 1H NMR spectral profiles of 1Rh in toluene-d8 at 20 degrees C in the presence of enantiomer mixtures of C76 of different optical purities, an absolute Deltaepsilon value of 58.5 M-1 cm-1 at 330 nm was obtained for enantiomerically pure C76.     

Semibiological molecular machine with an implemented "AND" logic gate for regulation of protein folding

A semibiological molecular machine with an implemented "AND" logic gate was developed, which was capable of controlling the folding process of proteins in response to ATP and light as input stimuli. The molecular design made use of a genetically engineered chaperonin GroEL bearing, at both entrance parts of its cylindrical cavity, cysteine residues, which were functionalized by an azobenzene derivative to construct photoresponsive mechanical gates (azo-GroEL). This engineered chaperonin trapped denatured green fluorescent protein (GFP(denat)) and prohibited its refolding. However, when hosting azo-GroEL detected ATP (input stimulus 1) and UV light (input stimulus 2) at the same time, it quickly released GFP(denat) to allow its refolding. In contrast, reception of either input stimulus 1 or 2 resulted in only very slow or no substantial refolding of GFP(denat). Implementation of such "AND" logic gate mechanisms in mechanically driven biomolecular systems is an important step toward the design of secured drug delivery systems.