Multicanonical parallel simulations of proteins with continuous potentials

The determination of the three‐dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its amino acid sequence, which suggests that it might be possible to determine the 3D structure of a protein from its amino acid sequence by pure computations. As a step toward that goal, in this article we present a simple approach for parallelization of multicanonical Monte Carlo simulations of proteins with continuous potentials. Our method is based on the parallel calculation of the protein energy function. The algorithm is tested by simulated annealing and multicanonical simulations of two small peptides, and known results are reproduced accurately. An acceptable degree of parallelization can be achieved in the simulation of Protein L using up to 30 PCs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1287–1296, 2001     

Redox equilibria of iron oxides in aqueous-based magnetite dispersions: effect of pH and redox potential

The effect of pH and redox potential on the redox equilibria of iron oxides in aqueous-based magnetite dispersions was investigated. The ionic activities of each dissolved iron species in equilibrium with magnetite nanoparticles were determined and contoured within the Eh-pH framework of a composite stability diagram. Both standard redox potentials and equilibrium constants for all major iron oxide redox equilibria in magnetite dispersions were found to differ from values reported for noncolloidal systems. The "triple point" position of redox equilibrium among Fe(II) ions, magnetite, and hematite shifted to a higher standard redox potential and an equilibrium constant which was several orders of magnitude higher. The predominant area of magnetite stability was enlarged to cover a wider range of both pH and redox potentials as compared to that of a noncolloidal magnetite system.     

Effects of reduction temperature and metal-support interactions on the catalytic activity of Pt/gamma-Al2O3 and Pt/TiO2 for the oxidation of CO in the presence and absence of H2

TiO2- and gamma-Al2O3-supported Pt catalysts were characterized by HRTEM, XPS, EXAFS, and in situ FTIR spectroscopy after activation at various conditions, and their catalytic properties were examined for the oxidation of CO in the absence and presence of H2 (PROX). When gamma-Al2O3 was used as the support, the catalytic, electronic, and structural properties of the Pt particles formed were not affected substantially by the pretreatment conditions. In contrast, the surface properties and catalytic activity of Pt/TiO2 were strongly influenced by the pretreatment conditions. In this case, an increase in the reduction temperature led to higher electron density on Pt, altering its chemisorptive properties, weakening the Pt-CO bonds, and increasing its activity for the oxidation of CO. The in situ FTIR data suggest that both the terminal and bridging CO species adsorbed on fully reduced Pt are active for this reaction. The high activity of Pt/TiO2 for the oxidation of CO can also be attributed to the ability of TiO2 to provide or stabilize highly reactive oxygen species at the metal-support interface. However, such species appear to be more reactive toward H2 than CO. Consequently, Pt/TiO2 shows substantially lower selectivities toward CO oxidation under PROX conditions than Pt/gamma-Al2O3.     

Propane fuel cells using phosphoric-acid-doped polybenzimidazole membranes

Propane fuel cells using H(3)PO(4)-doped polybenzimidazole polymer membranes produce low and unsustainable current densities at temperatures up to 250 degrees C under anhydrous conditions. Stable intermediate species blocked the surface of noble metal anode catalysts, and the intermediate species could not react further into desorbable final products. In contrast, when water was introduced by light humidification (S(r) 0.08%) of the propane stream, sustainable and higher current densities were achieved. Water participated in the reaction sequence to form surface-bound hydrocarbon and then oxygen-containing intermediates and thereby generated CO and CO(2) as the only carbon-containing products.     

Counterion condensation and release in micellar solutions

Counterion condensation and release in micellar solutions are investigated by direct measurement of counterion concentration with ion-selective electrode. Monte Carlo simulations based on the cell model are also performed to analyze the experimental results. The degree of counterion condensation is indicated by the concentration ratio of counterions in the bulk to the total ionic surfactant added, alpha< or =1. The ionic surfactant is completely dissociated below the critical micelle concentration (cmc). However, as cmc is exceeded, the free counterion ratio alpha declines with increasing the surfactant concentration and approaches an asymptotic value owing to counterion condensation to the surface of the highly charged micelles. Micelle formation leads to much stronger electrostatic attraction between the counterion and the highly charged sphere in comparison to the attraction of single surfactant ion with its counterion. A simple model is developed to obtain the true degree of ionization, which agrees with our Monte Carlo results. Upon addition of neutral polymer or monovalent salts, some of the surfactant counterions are released to the bulk. The former is due to the decrease of the intrinsic charge (smaller aggregation number) and the degree of ionization is increased. The latter is attributed to competitive counterion condensation, which follows the Hefmeister series. This consequence indicates that the specific ion effect plays an important role next to the electrostatic attraction.     

Catalytic Stereoinversion of L‐Alanine to Deuterated D‐Alanine

A combination of an achiral pyridoxal analogue and a chiral base has been developed for catalytic deuteration of L ‐alanine with inversion of stereochemistry to give deuterated D ‐alanine under mild conditions (neutral pD and 25 °C) without the use of any protecting groups. This system can also be used for catalytic deuteration of D ‐alanine with retention of stereochemistry to give deuterated D ‐alanine. Thus a racemic mixture of alanine can be catalytically deuterated to give an enantiomeric excess of deuterated D ‐alanine. While catalytic deracemization of alanine is forbidden by the second law of thermodynamics, this system can be used for catalytic deracemization of alanine with deuteration. Such green and biomimetic approach to catalytic stereocontrol provides insights into efficient amino acid transformations.     

Enantioselective Synthesis of Quaternary Carbon Stereocenters: Addition of 3‐Substituted Oxindoles to Vinyl Sulfone Catalyzed by Pentanidiums

A pentanidium‐catalyzed highly enantioselective conjugate addition of 3‐alkyloxindoles to phenyl vinyl sulfone has been demonstrated. This approach allows the construction of 3,3‐dialkyl‐substituted oxindole frameworks with high yield and excellent enantioselectivity (up to 99 %) under simple phase‐transfer conditions. A variety of oxindoles bearing all‐carbon quaternary stereogenic centers were obtained in the presence of 0.25 mol % pentanidium. Meanwhile, practicality was illustrated by a gram‐scale asymmetric synthesis of two 3,3‐dialkyl‐substituted oxindoles. The resulting adduct can be smoothly transformed to the natural product analogue in a short synthetic route.     

Serum exosomal microRNAs as novel biomarkers for hepatocellular carcinoma

Recent studies have shown that circulating microRNAs are a potential biomarker in various types of malignancies. The aim of this study was to investigate the feasibility of using serum exosomal microRNAs as novel serological biomarkers for hepatocellular carcinoma (HCC) in patients with chronic hepatitis B (CHB). We measured the serum exosomal microRNAs and serum circulating microRNAs in patients with CHB (n=20), liver cirrhosis (LC) (n=20) and HCC (n=20). Serum exosomal microRNA was extracted from 500 μl of serum using an Exosome RNA Isolation kit. The expression levels of microRNAs were quantified by real-time PCR. The expression levels of selected microRNAs were normalized to Caenorhabditis elegans microRNA (Cel-miR-39). The serum levels of exosomal miR-18a, miR-221, miR-222 and miR-224 were significantly higher in patients with HCC than those with CHB or LC (P<0.05). Further, the serum levels of exosomal miR-101, miR-106b, miR-122 and miR-195 were lower in patients with HCC than in patients with CHB (P=0.014, P<0.001, P<0.001 and P<0.001, respectively). There was no significant difference in the levels of miR-21 and miR-93 among the three groups. Additionally, the serum levels of circulating microRNAs showed a smaller difference between HCC and either CHB or LC. This study suggests that serum exosomal microRNAs may be used as novel serological biomarkers for HCC.     

Polymersomes Prepared from Thermoresponsive Fluorescent Protein–Polymer Bioconjugates: Capture of and Report on Drug and Protein Payloads

Polymersomes provide a good platform for targeted drug delivery and the creation of complex (bio)catalytically active systems for research in synthetic biology. To realize these applications requires both spatial control over the encapsulation components in these polymersomes and a means to report where the components are in the polymersomes. To address these twin challenges, we synthesized the protein–polymer bioconjugate PNIPAM‐b‐amilFP497 composed of thermoresponsive poly(N‐isopropylacrylamide) (PNIPAM) and a green‐fluorescent protein variant (amilFP497). Above 37 °C, this bioconjugate forms polymersomes that can (co‐)encapsulate the fluorescent drug doxorubicin and the fluorescent light‐harvesting protein phycoerythrin 545 (PE545). Using fluorescence lifetime imaging microscopy and Förster resonance energy transfer (FLIM‐FRET), we can distinguish the co‐encapsulated PE545 protein inside the polymersome membrane while doxorubicin is found both in the polymersome core and membrane.     

Hydrogen‐Bonding Induced Cooperative Effect on the Energy Transfer in Helical Polynorbornenes Appended with Porphyrin‐Containing Amidic Alanine Linkers

Polynorbornenes appended with porphyrins containing a range of different linkers are synthesized. The use of bisamidic chiral alanine linkers between the pending porphyrins and the polymeric backbone has been shown to bring the adjacent porphyrin chromophores to more suitable orientation for exciton coupling owing to hydrogen bonding between the adjacent linkers. The hydrogen bonding between the adjacent pendants in these polymers may induce a cooperative effect and therefore render single‐handed helical structures for these polymers. Such a cooperative effect is reflected in the enhancement of FRET efficiencies between zinc–porphyrin and free base porphyrin in random copolymers.