Solution conformation of gramicidin S: An intramolecular nuclear Overhauser effect study

Abstract

The solution conformation of gramicidin S in deuterated dimethyl sulfoxide was investigated by using the intramolecular nuclear Overhauser effect experiment. Experimental Overhauser enhancements were compared with predicted values for each ofthe nine most-stable conformations (M1-M9) calculated by Dygert et al on the basis of energy-minimization procedures [Dygert, M., Go, N. & Scheraga, H. A. (1975) Macromolecules 8,[750][751][752][753][754][755][756][757][758][759][760][761]. By using statistical hypothesis testing, the three lowestenergy conformations (MI, M2, and M3) were shown to give the best fit with the experimental data. All other conformations (M4-M9) were found to be inconsistent with the experimental data.Intramolecular nuclear Overhauser effects (NOEs) are very sensitive to interproton distances when dipole-dipole interaction is the predominant mechanism ofproton relaxation (1). Because of this distance dependence, NOE measurements have been used extensively in conformational studies of small molecules (1); however, their application to peptides is relatively recent (2-7).The cyclic decapeptide antibiotic gramicidin S has been the subject ofmany experimental [ref. 8 perature was 297 ± 1 K. In the NOE experiment, the resonance signal of interest was selectively presaturated for 4 sec before the observation pulse. The decoupler power was set such that the irradiation was highly selective; the decoupler power spillover to the neighboring resonance signals was less than 2% in general, as determined from the difference spectra. For the control spectrum, the irradiation frequency was set away from the spectral region by more than 2 kHz. The degree of saturation of the irradiated lines was 80-90%, and the observed NOEs were finally corrected for 100% saturation of the irradiated peak by dividing by the degree of saturation. One thousand scans were accumulated for each spectrum. To minimize the effects associated with spectrometer drift and to obtain clean difference spectra, the accumulation was alternated every eight scans between the control and the NOE experiments. A 0.5-Hz exponential line broadening was used in Fourier transforming the free induction decays. The NOE difference spectra were obtained by subtracting the control spectrum from the double resonance spectra. The NOE enhancements were calculated as fractional intensity changes for each resonance signal. For overlapping signals and for the C'H2 multiplet of D-phenylalanine, integrated intensities were used in computing the NOEs. RESULTS AND DISCUSSIONThe nuclear Overhauser effect experiment measures the steadystate effect of saturation of a specific spin transition or group of transitions on the intensities of other resonances in the NMR spectrum. The fractional change in the intensity of spin i when a spin s (or a group of such spins) is saturated can be computed by solving a set ofsimultaneous equations of the form (2) oijff(s) + I oyfj(s)where the summation on the right-hand side involves only the saturated spins. The oii and (ri...

Deuterium nuclear magnetic resonance investigation of the exchangeable sites on gramicidin A and gramicidin S in multilamellar vesicles of dipalmitoylphosphatidylcholine

“…Gramicidin S is a circular decapeptide that has been shown to adopt a pleated sheet structure stabilized by four intramolecular hydrogen bonds in nonaqueous solvents (Stern et al, 1968;Ovchinnikov et al, 1970;Rae et al, 1977) and in the solid state (Hull et al, 1978;Huang et al, 1981;Krauss & Chan, 1982a,b). This antibiotic has been shown to disrupt and solubilize lecithin liposomes (Finer et al, 1969;Pache et al, 1972;Wu et al, 1978).…”

Complexation and phase transfer of nucleic acids by gramicidin S

“…In view of the 2:1 stoichiometry of binding and the lipophilicity of the nucleic acid-GrS complexes, the interaction should involve apposition of the Orn side chains of GrS to adjacent phosphoryl groups of the nucleic acid backbone, with exposure of the hydrophobic face of the peptide to the solvent. From what is presently known of the solution conformation of the peptide (Ovchinnikov et al, 1970;Rae & Scheraga, 1978;Kuo et al, 1979;Huang et al, 1981;Krauss & Chan, 1982), a mode of binding to double-stranded DNA is proposed in which GrS is oriented with the peptide ring plane and ring minor axis parallel to the DNA helix axis, each peptide molecule thus forming up to eight interamide hydrogen bonds with the backbone moieties of its neighbors on opposite sides of the grooves. At saturation, the nucleic acid is then virtually ensheathed by bound peptide, the resultant complex being markedly hydrophobic.…”

Proton nuclear magnetic resonance study of an active pentapeptide fragment of ubiquitin

“…The side chains of Asn and Tyr appear to populate two rotamers predominantly, with a slight preference for one of the rotamers indicated in the case of Asn. Further investigations, especially involving intramolecular nuclear Overhauser effect experiments (Noggle & Schirmer, 1971;Krishna et al, 1978;Huang et al, 1981), 13C relaxation time measurements, and conformational energy calculations are in progress to gain more quantitative information on the solution dynamics of UB5. Ultimately, studies of various agonist and antagonist analogues of UB5 and their conformationally constrained derivatives are required to correlate its solution conformation to the biological activity.…”