Due to the critical role of DNA in the processes of the cell cycle, the structural and physicochemical properties of DNA have long been of concern. In the present work, the effect of interplay between the DNA duplex and metal ions in solution on the DNA structure and conformational flexibility is studied by comparing the structure and dynamic conformational behavior of a duplex in a normal form...

Earlier x-ray studies on dissolved linear DNA molecules were interpreted on the assumption that the molecules scattered as rigid rods. Improvement in equipment and advances in theory of the scattering from randomly oriented helices prompted us into a reinvestigation of this problem. Careful measurements were made on the scattering from both linear calf thymus DNA and from circular plasmid COP60...

Pheromonotropic neuropeptide, Pseudaletia pheromonotropin, is an 18 amino acid peptide with the sequence Lys-Leu-Ser-Tyr-Asp-Asp-Lys-Val-Phe-Glu-Asn-Val-Glu-Phe-Thr-Pro-Arg-Leu which is widely distributed in female moths of Bombyx mori. This peptide is structurally related to leucopyrokinin, an insect myotropic neuropeptide, responsible for melanization and reddish coloration hormone (MRCH) act...

We examined the 220-MHz NMR spectra for a series of oligopeptides derived from gamma-ethyl L-glutamate, an octapeptide based on beta-methyl L-aspartate, and a low molecular weight L-glutamate polymer ([unk]DP = 20) in deuterochloroform-trichloroacetic acid. A definite transition from folded to nonhelical forms was established for the glutamate systems. The aspartate behavior is explained by a p...

excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c, a case study. Biophys. Conformational fluctuations and electronic properties in myoglobin. A. Di Nola. Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Biophys. A. Di Nola. Molecular dynamics simulations of sperm whale myoglobin: effects of mutations...

Equilibrium twist angles and rotational barriers for the three isomeric phenylpyrroles were calculated by means of MNDO and AMI. In each case MNDO incorrectly predicts the perpendicular conformation as the most stable one. In agreement with experimental evidence AMI predicts only slight deviations from planarity and very low 0°-barriers (1-phenylpyrrole: 0 = 28°, E = F6 kJ mol"; 2-phenylpyrrole...

We apply conformational space annealing (CSA), an efficient global optimization method, to the study of protein-protein interaction. The CSA is incorporated into the Tinker molecular modeling package along with a B-spline method for CAPRI Round 5 experiments. We have used an energy function for the protein-protein interaction that consists of electrostatic interaction, van der Waals interaction...