In our earlier studies using quantum chemical methods we had proposed that propranolol has an extended structure. These results were confirmed using proton NMR. We have now carried out extensive magnetic resonance and model building studies to examine the interaction of this drug with model membranes. The effect of propranolol on organization of lipid bilayers has been studied using ESR spin labeling technique. Spin label Tempo and spin labeled stearic acid (5 SASL) have been used to monitor changes in the fluidity of model membranes. Presence of the drug is found to fluidize the lipids. In case of 0.2M dipalmitoyl phosphatidyl choline (DPPC), presence of drug (0.1M) is found to decrease the gel-liquid crystalline phase transition temperature by about 10°C. The order parameter measured from the spectrum of 5 SASL shows a 4% decrease on incorporation of the drug in membranes. I3C spin lattice relaxation time ( T I ) measurements have been carried out for different nuclear sites of the drug. The aromatic moiety shows a high degree of molecular rigidity when the drug is bound to the lipid bilayers. The oxypropanolamine group is however relatively flexible. It appears from these studies that the aromatic group binds strongly to the hydrophobic regions of the lipid bilayer, while the oxypropanolamine moiety remains relatively free and lies in the hydrophilic region. The 13C chemical shifts indicate the involvement of the @-hydroxyl group in hydrogen bonding with the lipids. The NH: group may be involved in electrostatic interactions with the negatively charged phosphate group of the lipid bilayers.

To validate the existing hypothesis put forward by Navarro et al., we performed single crystal X-ray diffraction structural analysis of a designed model peptide incorporating an unsubstituted achiral γ-aminobutyric acid: Boc-Pro-γ-Abu-OH (1) lacking C-terminal amide group. The analysis established existence of an overall unusual tightly folded topology stabilized by a conventional N(i)···H--N(i + 1) and an unconventional C(i)--H···O(i) type intramolecular hydrogen bonding interactions, encompassing a five-membered and a six-membered ring motifs, respectively. Moreover, in conjunction with Fourier transform infrared (FT-IR) absorption study in solid KBr, the results provided evidence that two conventional and one unconventional noncovalent intermolecular interaction stabilize a right-handed helical architecture generated via molecular self-assembly by translating the symmetry related molecules along the crystallographic b axis. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 927-931, 2010.

Model building, difference spectroscopy, and ' H and I3C N M R experiments have been carried out to study the binding of poly(L-Ser) with the polyribonucleotides poly(A) and poly(U) at pH 7.1. Studies have also been carried out with base paired duplexes poly(A)-poly(U). Peak doubling of C" and carbonyl resonances in the I3C N M R spectrum of poly(L-Ser) in presence of polyribonucleotides is observed. From the chemical shifts and the linewidth, it is concluded that the interaction occurs through hydrogen bonding between the nucleic acid bases and the peptide backbone. In case of poly(A) and poly(U) the hydrogen bonding scheme with peptide backbone is different from that in the base paired poly(A)-poly((/). The possible binding schemes of double stranded DNA and peptide backbone have been investigated using model building and potential energy calculations. The hydrogen bonding schemes discriminate between various base pairs and their sequence. It is concluded that protein backbone can play an important role in protein-nucleic acid recognition schemes.

An immunomodulating tetrapeptide, rigin (H-Gly-Gln-Pro-Arg-OH), has been examined for its secondary structure preferences through combined use of high-temperature unrestrained MD simulations in implicit water and 1D and 2D 1H NMR spectroscopy.The distribution of backbone torsion angles revealed the predominance of trans conformers across the Xaa-Pro peptide bond. The results of MD simulations revealed that of the five predicted families A-E, the predominant families, family A (92 structures), family C (63 structures) and family D (31 structures), could be complemented by extensive 1D and 2D 1H NMR parameters acquired in aqueous PBS solution. A survey of specific inter- and intraresidue NOEs substantiated the predominance of an unusual type VII beta-turn structure, defined by two torsion angles, i.e. psiGln approximately 155 degrees and psiPro approximately -65 degrees across the Gln-Pro segment. The proposed semi-folded kinked topology precluded formation of any intramolecular interaction, i.e. hydrogen bond or electrostatic interaction. Far-UV CD spectral characteristics of rigin in aqueous PBS solution and non-aqueous structure promoting organic solvents, TFE and TMP, revealed its strong solvent dependence. However, in aqueous PBS solution, the presence of a weak negative shoulder at approximately 234 nm could be ascribed to a small population with ordered, semi-folded topology.We propose that the plausible structural attributes may be exploited for design and rigidification of the bioactive conformation of this immunomodulator toward improved immunopharmacological properties.

A close examination of the crystal structure of tRNAPhe proposed by various groups reveals a great deal of discrepancy in the secondary structure of its acceptor end. The technique of energy minimization has been employed to study the preferred conformations and the flexibility of the pCpCpA fragment. Starting from various structures proposed for the -C-C-A end in tRNAPhc, the energy has been minimized as a function of 17 dihedral angles. A conformation where the terminal adenine is not stacked over the other two bases is found to be the most preferred conformation. This geometry is close to the refined structure proposed by the DUK group. Our results suggest a high degree of flexibility for the terminal adenosine unit in the -C-C-A segment. These findings are compared with the structure of -C-C-A in solution, as observed by nuclear magnetic resonance.