Partitioning of energy in the interaction of non-intercalating antibiotics (netropsin, netropsin without its cationic ends and two analogs of distamycin A) with different base sequences of B-DNA is studied here by the atom-atom potential technique and geometry optimization procedures. The results show that electrostatic forces contribute substantially to the stabilization energy as well as to the sequence specificity. The hydrogen-bonding term is also sequence specific and is significant in properly orienting the drug molecule. Relative roles of the hydrogen bonding and electrostatic interactions depend on the dielectric property of the medium.

We present here results on 260 pico seconds (ps) molecular dynamics (MD) simulation of substance P (SP) in hydrated bilayer of dimyristoyl phosphatidyl choline (DMPC) (39 molecules of DMPC with 776 water molecules). 260 ps MD simulation has been carried out in 0.001 ps time interval with united atom force field, using AMBER 4.0 package. Non bonded pair list was updated every 20 cycles using 12.5 Angstrom cut off distance. Analysis of MD data is done using our package ANALMD. The obtained models are presented using graphics package RASMOL. All simulations, analysis of MD data and graphics is done on INDIGO-2, R-4400 extreme graphics work station. Our results show no systematic change in order parameter, but reduction in transfraction of the chain torsional angles, compared to our earlier results on MD simulation on hydrated DMPC bilayer without SP. C-terminal and central peptide residues adopt partial helical conformation. Helix type as classified on the basis of H-bonds is between alpha and 3(10). The peptide backbone shows flexibility during heating runs. Later, it is stabilized and there was not much change in the spatial position of the backbone. Lipid matrix serves the role of immobilization of the peptide backbone in a preferred conformation.

We present models for the interaction of glucocorticoids: dexamethasone (DEX), dexamethasone-21-mesylate (DEXM) and deacylcortivazol (DAC) with the hexanucleotide sequence d(TGTTCT), (CORE sequence) found in the long terminal repeat of MMTV. These models are obtained by computer-aided geometry simulation with energy minimization technique, making use of the empirical potential energy functions. We have considered both intercalative A d nonintercalative binding. Differences in the glucocorticoid activity of these steroids are explained on the basis of stereochemical and energetic differences. A model is proposed for interaction of the steroid-receptor complex with the hormone-responsive element (HRE).

: Developing seeds of two chickpea varieties were collected on the 20th, 40th and 60th day after Ñowering (DAF) and analysed for trypsin inhibitors (TI). The varieties di †ered in their TI proÐles and activity units. The TI band and activity were not detectable at 20 DAF in the varieties Annigeri and BDN 9-3. Annigeri showed the highest total and speciÐc TI activity, and Ðve isoinhibitors at 40 DAF, which decreased to four at 60 DAF. The appearance and disappearance of TI bands during seed development indicate their speciÐc posttranslational modiÐcation and/or the presence of isolated gene groups.

This paper reports an ab inifio molecular-orbital (MO) study of binding of SH2 and SHwith Zn". The mechanism of binding of Zn" with these ligands is investigated using a detailed analysis of the energy decomposition and of the electronic distribution. The dependence of the results on the choice of the basis set for sulfur (in particular the effect of incorporation of diffuses p and d orbitals) on the geometry of ligand binding, the binding energy, and the proton affinity of SHare investigated. Comparison made with the corresponding results concerning the binding of OHz, OH-, and NH3 shows that sulfur binding is less favorable although more covalent. Both sulfur ligands show a marked preference for angular conformations for binding with the metal ion. The effect of Zn" binding on the ease of deprotonation of H2S is quite similar to the corresponding effect found earlier for H 2 0 .