Head-to-head dimerization of parallel beta helices in a synthetic model of the linear gramicidins

Conformational and structural analysis of the equilibrium between single- and double-strand ?-helix of aD,L-alternating oligonorleucine

Alternating sequences of D and L residues in peptides are directly related to the formation of several kinds of regular helical conformations usually called beta-helices. The major feature of these structures is that they can be associated with the transmembrane ion-conducting channel activity in some natural antibacterial peptides. The study of alternating D,L synthetic peptides is critical to understand how factors such as surrounding media, main chain length, type of side chain and terminal groups, among others, can determine the adoption of a specific kind of beta-helix. Early studies pointed out that the peptides Boc-(D-NLeu-L-NLeu)(6)-D-MeNLe-L-Nl-D-Nl-L-Nl-OMe (Boc: tert-butyloxycarbonyl) and Boc-L-Nle-(D-Nle-L-Nle)(5)-D-MeNle-L-Nle-D-Nle-L-Nle-OMe adopt in chloroform a unique detectable conformation single beta(4.4)- and double beta(5.6) upward arrow downward arrow -helix, respectively. The influence of terminal groups on the final stable conformation of N-formylated peptides has been studied in this work. The initial basic NMR data analysis of a synthetic alternating D,L-oligopeptide with ten norleucines, N-methylated on the residue 7 and having HCO- and -OMe as terminal groups clearly indicates the coexistence of two different conformations in equilibrium. NMR data and molecular dynamics calculations point to a dimeric antiparallel beta-helix structure beta(5.6) upward arrow downward arrow for the main conformation. On the other hand, NMR data suggest a single beta-helix structure beta(4.4) for the second conformation. Finally, a thermodynamic analysis of the equilibrium between both conformations has been carried out by one-dimensional NMR measurements at ten different temperatures. The temperature at which 50% of dimer conformation is dissociated is 319 K. In addition, the dimer-monomer equilibrium curve obtained shows a DeltaG>0 for the whole range of studied temperatures, and its behavior can be considered similar to the thermodynamic denaturation protein processes.

A study of the conformational equilibrium of DL-oligophenylalanines in nonpolar solvents in the presence and absence of lipids by high-performance liquid chromatography

The usefulness of high-performance size-exclusion liquid chromatography (HPSEC) for the separation of dimeric and monomeric species of DL-alternating oligophenylalanines is demonstrated for the first time. The experimental data obtained as a function of time fit a simple dimer-monomer equilibrium in a nonpolar solvent such as tetrahydrofuran. A higher extent of monomerization and a decrease in the time required for reaching equilibrium were detected in the presence of either water or phosphatidylcholine. The analysis of the relative proportions of the two separated species under equilibrium conditions has allowed the influence of the oligopeptide chain length on the stability of dimeric species to be determined. The advantages of this methodology, in combination with spectroscopic techniques, in studies on autoassociating peptides are considered.

Analysis of the binding of Ca2+ to gramicidin A in ethanol in terms of the dimer-monomer conformational equilibrium

This study reports the first direct observation of the binding of Ca2+ to gramicidin A in ethanol, analysed in terms of the polypeptide dimer-monomer conformational equilibrium. High performance size-exclusion chromatography has been successfully used to elucidate the binding mechanism and to determine the rate constants as well as the stoichiometry of the processes involved. In addition, fluorescence intensity and anisotropy measurements have revealed a dependence of the number of accessible Ca2+-binding sites on the peptide concentration.

Gramicidin A--phospholipid model systems

Gramicidin A forms ion-conducting channels which can traverse the hydrocarbon core of lipid bilayer membranes. The structures formed by gramicidin A are among the best characterized of all membrane-bound polypeptides or proteins. In this review a brief summary is given of the occurrence, conformation, and synthesis of gramicidin A, and of its use as a model for ion transport and the interaction of proteins and lipids in biological membranes.

Conformational species of gramicidin A in non-polar solvent. A kinetic and thermodynamic treatment in the absence and presence of phosphatidylcholine as studied by high-performance liquid chromatography

A kinetic and thermodynamic study has been carried out to characterize quantitatively the conformational equilibrium of gramicidin A (GA) in tetrahydrofuran at different peptide concentrations in the absence and presence of egg yolk phosphatidylcholine by using size-exclusion high-performance liquid chromatographic analysis. In the absence of lipid, the experimental data fit a simple dimer-monomer equilibrium, the rate and equilibrium constants for the dissociation process being (1.6 +/- 0.7) X 10(-7) s-1 and (8.5 +/- 0.3) X 10(-6) M, respectively. A higher extent of monomerization and a decrease in the time required for reaching equilibrium are detected in the presence of phospholipid, the kinetic and thermodynamic effects depending on both lipid and GA concentrations. In order to account for these observations a cyclic equilibrium mechanism is proposed which is analysed in terms of four conformational species, namely, free monomer, free dimer, lipid-bound monomer and lipid-bound dimer. The results obtained are discussed in relation to recent literature data on lipid-protein interactions.