The solution structure of the 38 amino acid C-terminal region of the precursor for the HPLC-6 antifreeze protein from winter flounder has been investigated with molecular dynamics using the AMBER software. The simulation for the peptide in aqueous solution was carried out at a constant temperature of 0 degree C and at atmospheric pressure. The simulation covered 120 ps and the results were analyzed based on data sampled upon reaching a stable equilibrium phase. Information has been obtained on the quality of constant temperature and pressure simulations, the solution structure and dynamics, the hydrogen bonding network, the helix stabilizing role of terminal charges and the interaction with the surrounding water molecules. The Lys18-Glu22 interactions and the terminal charged residues are found to stabilize a helical structure with the side chains of Thr2, Thr13, Thr24 and Thr35 equally spaced on one side of the helix. The spacing between oxygen atoms in the hydroxyl group of the threonine side chains exhibits fluctuations of the order of 2-3 A during the 120 ps of simulation, but values simultaneously close to the repeat distance of 16.6 A between oxygen atoms along the [0112] direction in ice are observed. Furthermore, two engineered variants were studied using the same simulation protocol.

No abstract

No abstract

Application of a new chemometric system, SPECTRE, to quantitative structureactivity relationship (QSAR) analysis in agricultural drug design has been studied. The SPECTRE system was employed to analyze experimental data by calculating a statistical predictive model using an evolution of the PLS (Partial Least Squares) regression method. This new modeling method, which does not need any a priori knowledge about the chemistry involved, is compared with multi-linear regression (MLR) analysis where the performance depends upon knowledge provided by the researcher. The SPECTRE system is shown to be able to produce similar or even superior results when compared with the conventional method.

MO calculations were carried out for CH3SCl, C6H5SCl, and related compounds with the S–Cl group by the CNDO/2 or the ASMO-SCF method. The absorption bands in the 300–400 nm region observed were assigned to the σS-Cl*←nS transition in view of transition energy and oscillator strength. Such characteristic bands are attributed to the extraordinarily low energy level of the σS-Cl* orbital.