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. At 300 K, T. celer L30e is less flexible than its mesophilic homologue, and this difference becomes more pronounced at 350 K. Salt bridge networks, one triad and one hexad, are present at the surface of T. celer L30e. The ion pairs forming these salt bridges maintain close contact at a higher temperature, suggesting that these networks contribute to the protein’s hyperthermal stability. By contrast, we found no such networks to be present in yeast L30e. For charged residue I in T. celer L30e, the ΔΔGsolvI value and its corresponding ΔECoulI value possess opposite signs. This indicates that for T. celer L30e, a change in the solvation free energy of a charged residue due to increasing temperature is compensated by a change in the residude’s Coulombic interaction energy with the rest of the protein.

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. Like all SeW genes identified in different species, chicken SeW contains one well-conserved selenocysteine (Sec) at the 13th position encoded by the UGA codon. The proposed glutathione (GSH)-binding site at the Cys(37) of SeW is not conserved in the chicken, but Cys(9) and Sec(13), with possible GSH binding, are conserved in SeWs identified from all species. There are 23-59% and 50-61% homology in cDNA and deduced AA sequences of SeW, respectively, between the chicken and other species. The predicted secondary structure of chicken SeW mRNA indicates that the selenocysteine insertion sequence element is type II with invariant adenosines within the apical bulge. The SeW mRNA expression is high in skeletal muscle followed by brain, but extremely low in other tissues from chickens fed a commercial maize-based diet. The SeW gene is ubiquitously expressed in heart, skeletal muscle, brain, testis, spleen, kidney, lung, liver, stomach and pancreas in chickens fed a commercial diet supplemented with sodium selenite. These results indicate that dietary selenium supplementation regulates SeW gene expression in the chicken and skeletal muscle is the most responsive tissue when dietary Se content is low.

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. The size of the proteins is represented by the mean radius of gyration (Rg ), which follows the Flory scaling law, Rg ∝ Nν. The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, |qi| ≥ 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range.

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