A comparative study of the second-order hydrophobic moments for globular proteins: the consensus scale of hydrophobicity and the CHARMM partial atomic charges.

In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (δ). Proteins in Group I were spherical and those in Groups II and III were prolate.

Molecular dynamics simulations of a hyperthermophilic and a mesophilic protein L30e.

Molecular dynamics (MD) simulations were used to study the hyperthermophilic ribosomal protein L30e from archaeon Thermococcus celer at 300 and 350 K, and its mesophilic homologue, yeast L30e, at 300 K in explicit solvent for a period of 5.0 ns. Three trajectories obtained from the MD simulations were stable throughout the simulation period, such as total potential energy, radius of gyration, root-mean-square deviation, and secondary structures assignment.

Characterization and expression of chicken selenoprotein W.

As an essential trace element, selenium (Se) deficiency results in White Muscle Disease in livestock and Keshan disease in humans. The main objectives of this study were to clone and characterize the chicken selenoprotein W (SeW) gene and investigate SeW mRNA expression in chicken tissues. The deduced amino acid (AA) sequence of chicken SeW contains 85 AAs with UAG as the stop codon.

Key features for designing phosphodiesterase-5 inhibitors.

Phosphodiesterase superfamily is the key regulator of 3',5'-cyclic guanosine monophosphate (cGMP) decomposition in human body. Phosphodiesterase-5 (PDE-5) inhibitors, sildenafil, vardenafil and tadalafil, are well known oral treatment for males with erectile dysfunction. To investigate the inhibitory effects of traditional Chinese medicine (TCM) compounds to PDE-5, we performed both ligand-based and structure-based studies on this topic.

A novel strategy for designing the selective PPAR agonist by the "sum of activity" model.

Peroxisome proliferator-activated receptors alpha, delta and gamma are a collection of ligand-activated transcription factors crucial in lipid and glucose homeostasis. The involvement of these receptors in lipid metabolism makes them perfect therapeutic target for treating obesity and stroke. In this study, 'sum of activity' model was employed to design multi-target agonists.

Structure-based and ligand-based drug design for HER 2 receptor.

Human epidermal growth factor receptor 2, HER2, is a commonly over-expressed tyrosine kinase receptor found in many types of carcinoma. Despite that there are several HER2 inhibitors, namely Iressa, Tarceva and Tykerb, currently in clinical trials, all can cause several side effects. In this study, both structure-based and ligand-based drug design were employed to design novel HER2 inhibitors from traditional Chinese medicine (TCM).

A polarizer chip based on CMOS Cu-interconnect for optical telecommunications.

The construction by CMOS Cu-interconnect fabrication technology of an optical chip that performs the function of linear polarization is described. The chip consists of three rows of a one dimensional array of rods in a square lattice structure. The rods make use of the Cu-interconnects of a CMOS IC for this optical purpose.