An investigation of the conformation of peptide-T and its D-Ala analog by NMR and molecular dynamics simulations.

Peptide-T (ASTTTNYT) and its D-Ala analog (D-ASTTTNYT-NH2) have been designed to block the adsorption of HIV to CD4 receptors on T-cell lymphocytes, thus inhibiting viral infectivity. The conformation of these important peptides has been investigated by 2D-NMR and molecular dynamics simulations. The NMR studies in DMSO show that the peptides exist in solution as a mixture of conformations. beta-Turns and non-specific folded conformations are present in a small proportion in the ensemble of conformations, which is largely dominated by more or less extended structures. This result is in line with molecular dynamics simulations where beta-turns were found to occur with a low frequency and with energies 10 to 17 kcal/mole higher than the global minimum structure. Our findings differ from previous reports on the conformation of peptide-T determined by NMR.

NMR and molecular dynamics studies of tachykinins: conformation of the C-terminal pentapeptide of substance P(SP7-11).

Substance P belongs to the tachykinin family of neuropeptides which exhibit diverse pharmacological activity. The conformation of Phe1-Phe2-Gly3-Leu4-Met5-NH2 the C-terminal pentapeptide of substance P (SP7-11) has been studied by NMR and molecular dynamics (MD) methods. NMR studies were carried out both in DMSO-d6 and 95% H2O. Based on the observed chemical shifts, 3JNH alpha coupling constants, temperature coefficients of chemical shifts of NH resonances and the pattern of inter- and intraresidue NOE's, a predominantly extended backbone conformation has been deduced for the peptide in both DMSO and H2O. MD calculations carried out in vacuo indicate that the global minimum energy conformation of the molecule is folded with an intramolecular hydrogen bond between the protonated N-terminal and the C-terminal CONH2 group. The simulation shows that beta-turns are energetically unfavourable, while alpha-helices are seen to be unstable for the peptide. gamma-Bends at either Gly3 or Leu4 are the most preferred ones. Simulations carried out in DMSO as well as in water show a preference for a nearly extended conformation.

1H NMR investigation of the interaction of berberine and sanguinarine with DNA.

Interaction of the alkaloids, berberine and sanguinarine with calf thymus DNA has been studied by 1H NMR. All proton resonances of the two compounds have been assigned using 2D-COSY, NOESY and ROESY spectra. Berberine has been found to partially intercalate into DNA, while sanguinarine shows normal intercalation and also binds more firmly to DNA. The NMR experiments indicate that sanguinarine is more potent than berberine in its activity.

Conformational structure variations in DNA: a PCILO study.

Perturbative configuration interaction using localized orbital (PCILO) computations have been carried out on conformational preference of d(GpC) and d(CpG) units of Z-II DNA. By keeping the sugar pucker fixed in the crystallographic conformation, PCILO energies have been calculated as a function of torsion angles alpha and zeta around two P-O ester bonds with preselected values of beta, gamma and epsilon. The results indicate that the d(GpC) unit is energetically more stable than the d(CpG) unit and prefers a g+ t conformation in (alpha-zeta) hyper-space observed in the crystal structure. The d(CpG) unit, on the other hand, shows intrinsic preference for g-g- conformation with other torsion angles close to DNA-B structure. The possibility of d(GpC) unit responsible for the stability of Z-helix has been discussed.

Growth and behavior development in rural infants in relation to malnutrition and environment.

A group of 224 children from a rural cohort of 625 children registered from 1981 to 1983 in 10 villages of KV Block, Varanasi was assessed for morbidity, physical growth, and behavior development (Gesell's developmental schedule). By first birthday children of normal nutrition grade were reduced to one fourth and numbers in Grade II and III malnutrition doubled. This deterioration in nutritional status was probably due to high morbidity, i.e., gastrointestinal, respiratory infections, etc. The skull circumference was 43 cm at the age of one year, being lower by 3 cm than the average size. Children having Grades II and III malnutrition showed poor development in all the areas of behavior, i.e., motor, adaptive, language and personal social. Besides malnutrition, environmental factors like mother's involvement in teaching, encouraging the child, talking to him or being within the visual range; the parental education, their caste and the child's birth order contributed significantly to the development of the child during infancy.

Conformational studies on cimetidine and ranitidine by PCILO calculations and NMR spectroscopy.

The conformational characteristics of two H2-receptor antagonists, cimetidine and ranitidine, have been investigated by quantum mechanical PCILO method and the results indicate a folded conformation for cimetidine stabilized by intramolecular hydrogen bonding and an extended backbone conformation for ranitidine. NMR investigations carried out on these two drugs in solution, however, indicate a predominance of an extended conformation for both the molecules. The significance of this result has been discussed in terms of the activity of these two drugs. Besides these studies, NMR experiments have also been carried out on the drugs incorporated into the lipid bilayers to investigate the drug-lipid interaction. The results from this study suggest that the hydrophobic portion of the drugs is buried in the hydrophobic hydrocarbon chains of the lipid bilayer, while the terminal hydrophilic end of the drug lies at the lipid-water interface.

Conformational preference of Leu side chain in melanostatin in DMSO.

The solution conformation of melanostatin (Pro-Leu-Gly-NH2) in the neutral and protonated forms of DMSO has been monitored by one and two dimensional NMR techniques at 500 MHz. The temperature coefficients of the amide proton chemical shifts in conjunction with the observed NOESY spectra suggest that melanostatin in neutral form in DMSO adopts a backbone conformation such that leucine amide proton is buried by the proline ring and the side chain of leucine. Similar observation is made for protonated form of melanostatin in DMSO. The results of the present study are at variance with the earlier NMR studies which proposed a beta-turn structure for both the forms of melanostatin. There is, however, no evidence for the presence of beta-turn structure for both the forms of melanostatin in DMSO. In CDCl3 also Leu NH appears to be buried as evident from the solvent titration with DMSO and NOESY spectra.

Chemical synthesis, cloning and expression of human preproinsulin gene.

A 355 base pair DNA sequence coding for human preproinsulin has been assembled by joining 55 synthetic deoxyoligonucleotide fragments prepared by the modified phosphotriester methodology. Proinsulin was expressed under lac promoter control and truncated β -galactosidase 590 amino acid long sequence. The fused β-galactosidase proinsulin protein was produced in amount to 30 % of the total Escherichia coli proteins. It was also expressed in Μ13 bacteriophage and yeast system.