Molecular vibrations and normal modes in L-prolyl-glycyl-glycine using Wilson GF matrix method.

Collagen is one of the most important proteins containing mostly proline hydroxyproline and glycine. In collagen, approximately 33 percent of the amino acid residues are glycine and they occur at every third position, whereas remaining percentage is constituted by mainly proline or hydroxyproline and some part by alanine etc. having no definite positional placement in the chain. Thus, a study of conformation of proline and glycine containing dipeptides and tripeptides is important for understanding the conformation of collagen as a sequence of its constituent amino acids. In the present communication, we have studied spectral features of L-proline, L-prolyl-glycine (PG), L-prolyl-alanine (PA), L-glycylglycine (GG), Collagen and L-prolyl-glycyl-glycine (PGG). We have carried out detailed normal mode analysis of only PGG, because interpretation of spectra of other proline and glycine containing peptides can be treated as derivatives of this molecule. Urey-Bradley force field, which involves non-bonded interactions in the gem and cis configurations is used for calculation of normal modes. The "best-fit" set of constants are generated for PGG.

Effect of sulphur crosslinking on the stability and transition of triple helical DNA.

In continuation to our work on order-order and order-disorder transition in triple stranded DNA when it is bounded to netropsin, we report in this communication the stabilizing/destabilizing effect of disulphide linkage on the phase dynamics of the triplex using the amended Zimm-Bragg theory. It is observed that in contrast to the sequential triplex-->duplex -->single strand melting of the uncrosslinked triplex, crosslinking causes the triplex state to melt directly to the single stranded state, with no apparent intermediary of a duplex state. Since there is no overall difference in the enthalpy of crosslinked and uncrosslinked triplexes, the transition is entropy driven.

Normal vibrations and valence charge distribution in relation to bioactivity of gammexane.

Normal coordinate analysis has been made for gammexane using the Wilson's G-F matrix method with Urey-Bradley force field. Molecular orbital calculations using CNDO/2 method have also been carried out for the five isomers of hexachlorocyclohexane to give the valence charge densities on the atoms of the molecules. A toxicity parameter that takes into account a shape factor and the valence charge density on the atoms has been defined. On the toxicity scale so defined the gamma-isomer alone has a significant value.

Dynamics of Met5- and Leu5-enkephalin and their receptor binding activity in relation to morphine.

A complete normal coordinate analysis of Met5- and Leu5-enkephalins using Wilson's GF matrix method and Urey Bradley force field has been carried out to understand the dynamical behaviour of enkephalins. In addition, the charge distributions on different atoms of the two enkephalins and morphine using CNDO/2 method are also reported. The similarity in the charge distribution on the part of these two molecules is indicative of the possible interactions at the same receptor site as that of morphine and its derivatives. Apart from the topographical features and charge distribution, binding onto receptor site is not a static but a dynamic process and low frequency modes must play an important role in the recognition process. The significance of the out-of-plane amide VII band and other skeletal modes as characteristic of conformational states of Met5- and Leu5-enkephalins are discussed.

Conformational transitions and specific heat anomaly in poly(dG-dC) and its methylated analogue.

The Zimm and Bragg theory of the helix<-->coil transition has been modified to explain order<-->order transitions in polynucleotides, in particular B<-->Z<-->psi(-)<-->coil transitions in poly(dG-dC) and poly(dG-me5dC). Lambda anomalies in specific heat measurements around the transition point have also been explained by a further modification of the same theory. Theoretical results are found to be in good agreement with the experimental data. The nucleation parameter is consistent with the stabilization/destabilization of the ordered states (Z helix) under various environmental conditions, e.g. methylation of cytosine residue at C5 position or change in the cationic concentration of the solvent.