Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS

In order to stimulate the development of drugs against severe acute respiratory syndrome (SARS), based on the atomic coordinates of the SARS coronavirus main proteinase determined recently [Science 13 (May) (2003) (online)], studies of docking KZ7088 (a derivative of AG7088) and the AVLQSGFR octapeptide to the enzyme were conducted. It has been observed that both the above compounds interact with the active site of the SARS enzyme through six hydrogen bonds. Also, a clear definition of the binding pocket for KZ7088 has been presented. These findings may provide a solid basis for subsite analysis and mutagenesis relative to rational design of highly selective inhibitors for therapeutic application. Meanwhile, the idea of how to develop inhibitors of the SARS enzyme based on the knowledge of its own peptide substrates (the so-called "distorted key" approach) was also briefly elucidated.     

Using complexity measure factor to predict protein subcellular location

Summary. Recent advances in large-scale genome sequencing have led to the rapid accumulation of amino acid sequences of proteins whose functions are unknown. Because the functions of these proteins are closely correlated with their subcellular localizations, it is vitally important to develop an automated method as a high-throughput tool to timely identify their subcellular location. Based on the concept of the pseudo amino acid composition by which a considerable amount of sequence-order effects can be incorporated into a set of discrete numbers (Chou, K. C., Proteins: Structure, Function, and Genetics, 2001, 43: 246–255), the complexity measure approach is introduced. The advantage by incorporating the complexity measure factor as one of the pseudo amino acid components for a protein is that it can more effectively reflect its overall sequence-order feature than the conventional correlation factors. With such a formulation frame to represent the samples of protein sequences, the covariant-discriminant predictor (Chou, K. C. and Elrod, D. W., Protein Engineering, 1999, 12: 107–118) was adopted to conduct prediction. High success rates were obtained by both the jackknife cross-validation test and independent dataset test, suggesting that introduction of the concept of the complexity measure into prediction of protein subcellular location is quite promising, and might also hold a great potential as a useful vehicle for the other areas of molecular biology.     

EEG dynamics reflect the distinct cognitive process of optic problem solving

This study explores the changes in electroencephalographic (EEG) activity associated with the performance of solving an optics maze problem. College students (N = 37) were instructed to construct three solutions to the optical maze in a Web-based learning environment, which required some knowledge of physics. The subjects put forth their best effort to minimize the number of convexes and mirrors needed to guide the image of an object from the entrance to the exit of the maze. This study examines EEG changes in different frequency bands accompanying varying demands on the cognitive process of providing solutions. Results showed that the mean power of θ, α1, α2, and β1 significantly increased as the number of convexes and mirrors used by the students decreased from solution 1 to 3. Moreover, the mean power of θ and α1 significantly increased when the participants constructed their personal optimal solution (the least total number of mirrors and lens used by students) compared to their non-personal optimal solution. In conclusion, the spectral power of frontal, frontal midline and posterior theta, posterior alpha, and temporal beta increased predominantly as the task demands and task performance increased.     

iRNA-Methyl: Identifying N-methyladenosine sites using pseudo nucleotide composition

Occurring at adenine (A) with the consensus motif GAC, N⁶-methyladenosine (m⁶A) is one of the most abundant modifications in RNA, which plays very important roles in many biological processes. The nonuniform distribution of m⁶A sites across the genome implies that, for better understanding the regulatory mechanism of m⁶A, it is indispensable to characterize its sites in a genome-wide scope. Although a series of experimental technologies have been developed in this regard, they are both time-consuming and expensive. With the avalanche of RNA sequences generated in the postgenomic age, it is highly desired to develop computational methods to timely identify their m⁶A sites. In view of this, a predictor called “iRNA-Methyl” is proposed by formulating RNA sequences with the “pseudo dinucleotide composition” into which three RNA physiochemical properties were incorporated. Rigorous cross-validation tests have indicated that iRNA-Methyl holds very high potential to become a useful tool for genome analysis. For the convenience of most experimental scientists, a web-server for iRNA-Methyl has been established at http://lin.uestc.edu.cn/server/iRNA-Methyl by which users can easily get their desired results without needing to go through the mathematical details.     

Kinetic mechanism of the cytosolic malic enzyme from human breast cancer cell line.

The kinetic mechanism of the cytosolic NADP(+)-dependent malic enzyme from cultured human breast cancer cell line was studied by steady-state kinetics. In the direction of oxidative decarboxylation, the initial-velocity and product-inhibition studies indicate that the enzyme reaction follows a sequential ordered Bi-Ter kinetic mechanism with NADP+ as the leading substrate followed by L-malate. The products are released in the order of CO2, pyruvate, and NADPH. The enzyme is unstable at high salt concentration and elevated temperature. However, it is stable for at least 20 min under the assay conditions. Tartronate (2-hydroxymalonate) was found to be a noncompetitive inhibitor for the enzyme with respect to L-malate. The kinetic mechanism of the cytosolic tumor malic enzyme is similar to that for the pigeon liver cytosolic malic enzyme but different from those for the mitochondrial enzyme from various sources.     

Oxidative stress is the master operator of drug and chemically-induced programmed and unprogrammed cell death: Implications of natural antioxidants in vivo

ROS, RNS, BRIs and ROS-RNS hybrids are produced during drug or chemical metabolism in vivo. These reactive species are instrumental to the culmination of cellular oxidative stress (OS). OS, once turned on, does not spare any vital intracellular macromolecule, such as glutathione, DNA, RNA, proteins, enzymes, lipids and ATP. Since concentration gradients of such components are very delicately balanced for normal cellular functioning, a gross perturbation leads to cell injury and cell death. Abundant evidence now suggests that intracellular antioxidants keep OS in check and maintain homeostasis. Our laboratory has focused on the role of OS in orchestrating various forms of cell death during drug and chemically-induced target organ toxicity and their counteraction by various natural or synthetic antioxidants in in vivo models. Despite complexity of the in vivo models, results show that metabolism of xenobiotics are invariably associated with different degrees of OS and natural antioxidants such as grape seed extract, bitter melon extract (Momordica charantia) and N-acetylcysteine (NAC) which were very effective in counteracting organ toxicities by minimizing events linked to OS (lipid peroxidation and total glutathione), and CAD-mediated DNA fragmentation. Phytoextract exposure rescued cells from toxic assaults, protected genomic integrity, and minimized apoptotic, necrotic and apocrotic (oncotic necrosis) cell deaths. Pre-exposure mode was more effective than post-exposure route. Overall scenario suggests that OS may have been the prime modulator of death and/or survival programs, whereas, antioxidants may have imparted a dual role in either erasing death signals or reviving survival signals, and a combination of antioxidants may be more beneficial than a single entity to influence a number of intracellular events operating simultaneously to neutralize chaotic toxicological consequences.     

Hepatoprotective activity of tocha, the stems and leaves of Ampelopsis grossedentata, and ampelopsin

Hepatoprotective effect of the leaves and stems of Ampelopsis grossedentata together with its main constituent, ampelopsin, were examined on D-galactosamine induced liver injury in rats. The diet containing 50% ethanolic extract (1%) and ampelopsin (0.1%) markedly suppressed the increase of LDH, ALT, AST, alpha-tocopherol levels and GSG/GSSH caused by GalN treatment. These results suggested that ampelopsin from Tocha acted to prevent the oxidative stress in vivo that may have been due to active oxygen species formed by a macrophage by the action of GalN.     

Development of an immunosensor for human ferritin, a nonspecific tumor marker, based on surface plasmon resonance

A direct human ferritin immunosensor was developed using anti-human ferritin monoclonal antibodies (MAbs) immobilized on the gold surface of a self-assembled surface plasmon resonance (SPR) apparatus. A kind of self-assembled monolayer (SAM) prepared by cystamine-glutaraldehyde method was applied to immobilize the MAbs. The reusability of the sensor chip adopting the SAM was found to be better than the other immobilization methods including adsorption, protein A, concanavalin A method. Ten cycles of measurements could be performed on the same chip regenerated with a 0.1M HCl solution. A linear relationship existed between the angle shifts (millidegrees) and the log values of ferritin concentrations in the range from 0.2 to 200 ng/ml in buffer and human serum. When used for 15 days, the angle shifts were all >95% of those on the response at the first day. A 10 M NaOH solution was used for clearing nonspecific binding in human serum. Correlation coefficient was 0.991 between this SPR method and chemiluminescent immunoassay for determination of ferritin in clinical human serum samples. The SPR sensor offers advantages of simplicity of immobilization, high sensitivity, high specificity, low sample requirement, high reusability, no label and no pretreatment etc.     

Ionic liquid ethanol sensor

Ionic liquids containing lithium methylsulfonyl group were prepared from the precursors poly(propylene glycol)-block-(ethylene glycol)-block-(propylene glycol)-bis(2-aminopropyl ether) with different molecular weight. These liquids revealed excellent electrical conductivity in the temperature range -25 to 85 degrees C. Also, they exhibited a high boiling temperature and hence a low vapor pressure in ambient condition. Additionally, they showed a high fluidity with their viscosities being comparative with that of water. To determine the sensitivity of an ethanol sensor by using these ionic liquids, these liquids were subjected into a sequential electrochemical tests with nickel electrodes which performed a high sensitivity for the ethanol sensor. It was found that only the derivative with low molecular weight could detect ethanol. Furthermore, a linear relationship between the response current and the concentration of ethanol was constructed. The detection limit was found to be 0.13% (v/v) and its response time was 336 s.     

Integrative genomics based identification of potential human hepatocarcinogenesis-associated cell cycle regulators: RHAMM as an example

DNA microarray has been widely used to examine gene expression profile of different human tumors. The information generated from microarray analysis usually represents the overall range of cancer-associated abnormality associated with gene regulation. In order to identify key regulatory genes involved in carcinogenesis of human cancer, hypothesis driven data mining of the microarray data plus experimental validation becomes a critical approach in the post-genome era. Here, we present an integrative genomic analysis of published microarray data and homolog gene database. Over 20,000 genes were examined to reveal 16 genes specific to vertebrates, cell cycle G2/M regulated, and overexpressed in human HCC. Using Affymetrix microarray analysis, we found that all 16 genes were up-regulated in human HCC. Among these 16 genes, we experimentally validated the up-regulation of receptor for hyaluronan-mediated motility (RHAMM) in different cell model systems. We first confirmed elevation of RHAMM in the G2/M phase of synchronized HeLa cells. We also found that RHAMM had an elevated level of expression in all the HCC samples we examined and it was induced during the G2/M phase of regenerating mouse hepatocytes after partial hepatectomy. Thus, the expression of RHAMM appears to be tightly regulated during mammalian cell cycle G2/M progression. The ectopic overexpression of RHAMM in 293T cells resulted in the accumulation of cells at G2/M phase. RHAMM-induced mitotic arrest of cells was predominantly in the prophase. Taken together, using an integrated functional genomic approach, we have uncovered a set of genes that may play specific roles in cell cycle progression and in HCC development. To elucidate the function of these genes in cell cycle regulation may shed light on the control mechanism of human HCC in the future.