The structure of crystalline and membrane-bound gramicidin A by vibrational analysis

Proposed Mechanism for H(II) Phase Induction by Gramicidin in Model Membranes and Its Relation to Channel Formation

A model is proposed for the molecular mechanism of H(II) phase induction by gramicidin in model membranes. The model describes the sequence of events that occurs upon hydration of a mixed lipid/gramicidin film, relating them to gramicidin channel formation and to relevant literature on gramicidin and lipid structure.

Conformation and orientation of gramicidin a in oriented phospholipid bilayers measured by solid state carbon-13 NMR

Three analogues of the helical ionophore gramicidin A have been synthesized with (13)C-labeled carbonyls ((13)C=O) incorporated at either Gly(2), Ala(3), or Val(7). A fourth compound incorporated (13)C at both the carbonyl and alpha-carbon of Gly(2) within the same molecule. These labels were studied using solid-state, proton-enhanced, (13)C nuclear magnetic resonance (NMR) in hydrated dispersions of dimyristoylphosphatidylcholine (DMPC)-gramicidin A. The dispersions were aligned on glass coverslips whose orientation to the magnetic field could be varied through 180 degrees . The orientation dependence of the NMR spectrum was used to obtain an accurate measurement of the (13)C chemical shift anisotropy (CSA), and in the case of the fourth compound, the (13)C-(13)C dipolar coupling constant. From the measured CSA and estimates of the orientation of the (13)C shielding tensor, we are able to determine the direction of the (13)C=O bonds and to compare these with the predictions of the various reported models for the configuration of gramicidin A in phospholipid bilayers. Our results are consistent with the left-handed pipi(6.3) (LD) single-stranded helix (Urry, D. W., J. T. Walker, and T. L. Trapane. 1982. J. Membr. Biol. 69:225-231). The right-handed pipi(6.3) (LD) single-stranded helix observed for gramicidin A in sodium dodecyl sulfate micelles (Arseniev, A. S., I. L. Barsukov, V. F. Bystrov, A. L. Loize, and Yu A. Ovchinnikov. 1985. FEBS (Fed. Eur. Biochem. Soc.) Lett. 186:168-174) yields a poorer fit to the data. However, the width of the carbonyl resonances suggests a distribution of molecular geometries possibly resulting from a spread in the helix pitch and handedness. Double-stranded helices and beta sheet structures are excluded. In dispersions in which the lipid is in the L(alpha) phase, the gramicidin A undergoes rapid reorientation about an axis which is centered on the normal to the plane of the coverslips. When the supporting lipid is in the L(beta') phase the helices are rigid on the timescale of (13)C-NMR. The configuration of gramicidin A is unaltered by L(alpha)-L(beta') phase transition of the bilayer lipid.

Vibrational spectroscopic studies of L,D-alternating phenylalanine peptides

Infrared and Raman spectra of Boc-(D-Phe-L-Phe)n-OMe, with n = 4 and 5, and Boc-L-Phe-(D-Phe-L-Phe)7-OMe, have been obtained in crystalline and solution states. Based on the earlier spectroscopic studies on Boc-(L-Val-D-Val)n-OMe, with n = 4, 6 and 8, and the predictions from the normal-mode calculations of double-stranded beta-helix conformations, structures have been assigned for the three oligopeptides. In the crystalline state, all three oligopeptides have a double-stranded increases decreases beta 5.6 structure. Spectra from chloroform solution indicate that the solid-state conformation is retained in this solvent for all three oligopeptides.

Environments and conformations of tryptophan side chains of gramicidin A in phospholipid bilayers studied by Raman spectroscopy

Raman spectroscopy has been used to investigate the hydrophobic interaction of the indole ring with the environments, the water accessibility to the N1H site, and the conformation about the C beta-C3 bond for the four tryptophan side chains of gramicidin A incorporated into phospholipid bilayers. Most of the tryptophan side chains of the head-to-head helical dimer transmembrane channel are strongly interacting with the lipid hydrocarbon chains, and the hydrophobic interactions for the rest increase with increasing hydrocarbon chain length of the lipid. One tryptophan side chain (probably Trp-15) is accessible to water molecules, another (Trp-9) is deeply buried in the bilayer and inaccessible, and the accessibilities of the remaining two (Trp-11 and Trp-13) depend on the bilayer thickness. The torsional angle about the C beta-C3 bond is found to be +/- 90 degrees for all the tryptophans irrespective of the membrane thickness. Binding of the sodium cation to the channel does not change the torsional angles but decreases the water accessibilities of two tryptophans (Trp-11 and Trp-13) considerably. In conjunction with a slight spectral change in the amide III region, it is suggested that the sodium binding causes a partial change in the main-chain conformation around Trp-11 and Trp-13, which results in the movements of these side chains toward the bilayer center. Two models consistent with the present Raman data are proposed for the tryptophan orientation in the dominant channel structure.

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.

Conformations of gramicidin A and its 9,11,13,15-phenylalanyl analog in dimethyl sulfoxide and chloroform

In order to understand the difference in single channel behavior of gramicidin A as compared to that of gramicidin M- which is the mirror image of gramicidin M (all four tryptophanyl residues substituted by phenylalanine), conformational investigations were made under several experimental conditions. It is shown that, when examined under identical conditions, both molecules adopt the same conformations which could be identified in dimethyl sulfoxide (DMSO) and chloroform. In DMSO the conformation is based on a succession of beta-turns while in chloroform gramicidin A and M- can adopt a dimeric hybrid structure: a double helix terminated by two single-stranded helices involving the N- and C-terminal parts, respectively. It is therefore concluded that the difference in the energy profile between both gramicidins which was deduced from the ion transfer data has its origin in the nature of the aromatic side chains.

Vibrational analysis of the structure of gramicidin A. II. Vibrational spectra

Raman and infrared spectra have been obtained of gramicidin A (GA) in the crystalline state both in the native form and complexed with CsSCN and KSCN, in solution in dioxane, and incorporated into lipid vesicles. Based on predictions from normal mode calculations of a number of relevant single- and double-stranded beta-helix conformations (Naik and Krimm, 1986), it has been possible to assign the structures of GA that are present under the above conditions. In the crystalline state, native GA has a double-stranded increases decreases beta 5.6 structure, whereas complexes with CsSCN or KSCN adopt a increases decreases beta 7.2 structure. In dioxane solution, the increases decreases beta 5.6 structure predominates. In lipid vesicles, the single-stranded beta 6.3-helix is found, which converts to a double-stranded helix on drying the sample. These results support our previous studies in showing that normal mode analysis can be a powerful technique in obtaining three-dimensional structural information from vibrational spectra.

Vibrational analysis of the structure of gramicidin A. I. Normal mode analysis

Normal mode frequencies have been calculated for single-stranded beta 4.4 and beta 6.3 and for double-stranded increases decreases beta 5.6, increases decreases beta 7.2, increases increases beta 5.6, and increases increases beta 7.2 helices that are possible models for the structure of gramicidin A. The force field used in the calculations is one that reproduces the frequencies of model polypeptide chain structures to about +/- 5 cm-1, and is therefore expected to provide meaningful distinctions between these conformations. The calculations predict significant differences in the infrared and Raman spectra of these beta-helices, suggesting that they should be identifiable from their spectra (which is shown in the following paper to be the case). The most sensitive region is that of the amide I frequencies, where the predicted patterns of intense infrared mode, infrared splittings, and intense Raman mode provide a characteristic identification of each of the above structures.

The influence of proteins and peptides on the phase properties of lipids

This paper reviews model membrane studies on the modulation of the macroscopic structure of lipids by lipid-protein interactions, with particular emphasis on the gramicidin molecule. This hydrophobic peptide has three main effects on lipid polymorphism: (1) in lysophosphatidylcholine it triggers a micellar to bilayer transition, (2) in phosphatidylethanolamine it lowers the bilayer to hexagonal HII phase transition temperature and (3) in phosphatidylcholine and other bilayer preferring lipids it is able to induce the formation of an HII phase. From experiments in which the gramicidin molecule was chemically modified it can be concluded that the tryptophan residues play a determining role in the peptide-induced changes in polymorphism. The experimental data lead to the proposal that gramicidin molecules have a tendency to self-associate, possibly mediated by tryptophan-tryptophan interactions and organize into tubular structures such as found in the HII phase.

Structure of gramicidin A

Gramicidin A, a hydrophobic linear polypeptide, forms channels in phospholipid membranes that are specific for monovalent cations. Nuclear Magnetic Resonance (NMR) spectroscopy provided the first direct physical evidence that the channel conformation in membranes is an amino terminal-to-amino terminal helical dimer, and circular dichroism (CD) spectroscopy has shown the sensitivity of its conformation to different environments and the structural consequences of ion binding. The three-dimensional structure of a gramicidin/cesium complex has been determined by x-ray diffraction of single crystals using single wavelength anomalous scattering for phasing. The left-handed double helix in this crystal form corresponds to one of the intermediates in the process of folding and insertion into membranes. Co-crystals of gramicidin and lipid that appear to have gramicidin in their membrane channel conformation have also been formed and are presently under investigation. Hence, we have used a combination of spectroscopic and diffraction techniques to examine the conformation and functionally-related structural features of gramicidin A.