In this study, a novel residue-residue contacts prediction approach based on evolutionary computation is presented. The prediction is based on four amino acids properties. In particular, we consider the hydrophobicity, the polarity, the charge and residues size. The prediction model consists of a set of rules that identifies contacts between amino acids.

in the present work, the structural and electronic properties, and conductivity of (5,5) and (6,6) single walled carbon nanotubes in the ground state have done by using the hartree-fock and density functional theory dft-b3lyp/6-31g* level. delocalization of charge density between the bonding or lone pair and antibonding orbitals calculated by nbo (natural bond orbital) analysis. these methods a...

While shielding in collisional, strongly magnetized (one-dimensional) plasmas obeys the standard Debye result, shielding in collisionless, immobile ion plasmas is far more complex than commonly believed. In some circumstances, the plasma will antishield a positive test charge; i.e., the plasma becomes more positive in the neighborhood of a positive test charge. When shielding does occur, it res...

Thermodynamical and optical properties of pure and electron beam irradiated (20, 80 and 100 kGy doses) liquid crystalline material cholesteryl pelargonate (nonanoate) have been investigated by differential scanning calorimeter, polarized light microscopy and ultraviolet-visible spectroscopy. Transition temperatures, enthalpies and entropies are found to be lowered due to the irradiation. A dono...

Dibasic amino acids and polyamines added to oat (Avena sativa L.) leaf protoplast isolation media decrease the RNase activity of extracted protoplasts relative to controls. This effect, which is manifested even when the added polyamine is removed by exhaustive dialysis prior to assay, is due to a prevention of the rise in RNase activity which usually follows protoplast isolation. Polyamines, bu...

The molecular details of how lipids influence final topological organization of membrane proteins are not well understood. Here, we present evidence that final topology is influenced by lipid-protein interactions most likely outside of the translocon. The N-terminal half of Escherichia coli lactose permease (LacY) is inverted with respect to the C-terminal half and the membrane bilayer when ass...

The product of gene 0.3 of bacteriophage T7, ocr, is a potent inhibitor of type I DNA restriction and modification enzymes. We have used biophysical methods to examine the mass, stability, shape and surface charge distribution of ocr. Ocr is a dimeric protein with hydrodynamic behaviour equivalent to a prolate ellipsoid of axial ratio 4.3 +/- 0.7:1 and mass of 27 kDa. The protein is resistant t...

The UL131A protein is part of a pentameric variant of the gcIII complex in the virion envelope of human cytomegalovirus (HCMV), which has been found essential for efficient entry into endothelial cells (ECs). Using a systematic mutational scanning approach, we aimed to define peptide motifs within the UL131A protein that contribute to EC infection. Mutant viruses were generated in which charged...