Structure of gramicidin A

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.

Fourier transform infrared study of proteins with parallel beta-chains

Deconvolved and second derivative Fourier transform infrared spectra of the proteins flavodoxin and triosephosphate isomerase have been obtained in the 1600 to 1700 cm-1 (amide I) region. To our knowledge these results provide the first experimental infrared data on proteins with parallel beta-chains. Characteristic absorption bands for the parallel beta-segments are observed at 1626-1639 cm-1 (strong) and close to 1675 cm-1 (weak). Previous theoretical studies based on hypothetical models with large, regular beta-sheets had suggested bands close to 1650 and 1666 cm-1. Our new assignments were confirmed by band area measurements, which yield conformational information in good agreement with results from X-ray diffraction data. The spectra were compared with corresponding spectra of concanavalin A and carboxypeptidase A. The first contains only antiparallel beta-segments, the second "mixed" beta-segments, with some strands lying antiparallel and others parallel. None of the observed amide I band frequencies assigned to parallel beta-chains occurs in the 1650 cm-1 region associated with helical segments.

The tertiary structure of azurin from Pseudomonas denitrificans as determined by Cu resonant diffraction using synchrotron radiation

The structure of Pseudomonas denitrificans azurin has been solved at 3.0 A resolution by film data collection methods using synchrotron radiation. Bijvoet pairs of reflections were collected using 8.98 keV radiation where both delta f' and delta f", the real and imaginary corrections to azurin's Cu prosthetic group scattering, respectively, are large, and using 8.00 keV radiation where these corrections are smaller. The Cu atom was located by difference Patterson syntheses and used to phase the observed protein structure-factor moduli of selected reflections. An atomic model of the protein was built using a restricted data set and phases for all observed reflections to 3.0 A resolution were subsequently calculated from the initial model. The atomic model was subsequently rebuilt using all observed data. The results of this work are presented here and illustrate the utility of synchrotron radiation phasing techniques in solving the structures of metalloproteins without recourse to multiple isomorphous replacement.

The interaction of Cl- with a gramicidin-like channel

Molecular dynamics simulations have been used to study the interaction of Cl- with a gramicidin-like channel. The results suggest that there is a high-energy barrier at the entrance of the channel, which would correspond to a permeability 10(-9)-times that of a cation of the same size. This could account for the cationic selectivity of the gramicidin channel and indicates that valence selectivity is kinetically controlled.

Uniformly oriented gramicidin channels embedded in thick monodomain lecithin multilayers

Phosphatidylcholine multilayers, containing 20% water by total sample weight and gramicidin/lipid molar ratios up to 1:40 were aligned by low temperature annealing (less than 60 degrees C) and mechanical stressing. We were able to obtain large (greater than 80 micron thick X 40 mm2 area) monodomain defect-free multilayers containing approximately 10(17) uniformly oriented gramicidin channels. The alignment of lipid multilayers was monitored by conoscopy and polarized microscopy. The smectic defects, which appeared during the alignment process, were identified and dissolved. The incorporation of gramicidin into the multilayers in the form of transmembrane channels was indicated by its circular dichroic (CD) spectrum. A well-defined CD spectrum of uniformly oriented gramicidin channels was obtained. The oriented samples will allow spectroscopic studies of the ion channel in its conducting state and diffraction studies of the channel-channel organization in the membrane.

Linear gramicidins at the air-water interface

The behavior of four linear gramicidins, which differ by the nature of their 9, 11, 13, and 15 aromatic residues, together with a covalent "head to tail" retro GA-DAla-GA dimer, has been examined at the air-water interface. It is shown that all four "monomers" have almost the same molecular area, which is compatible with either a single-stranded or a double-stranded helical model, whereas it is suggested that retro GA-DAla-GA could adopt another conformation. The surface potential measurements agree with those of different groups of molecules characterized by their single-channel behaviors.

Why is gramicidin valence selective? A theoretical study

Calculations contrasting the channel solvation energy for cesium ions and chloride ions associated with water in gramicidin-like channels are presented. The energy profile for the cation exhibits a deep well at the channel entrance; within the single file region the solvation energy is roughly constant. The anion exhibits a totally different energy profile. There is an energy barrier at the channel entrance; if the ion could surmount this barrier, it would be quite stable within the channel. At the channel entrance, the calculated solvation energy difference between anion and cation is approximately 15 kcal mol-1. This is completely consistent with the observation that chloride neither permeates nor blocks the channel since the estimated rate of ion entry would be approximately 0.01-10(-5) s-1, far slower than the rate at which the channel dimer dissociates into monomers.

How pore mouth charge distributions alter the permeability of transmembrane ionic channels

This paper investigates the effects that surface dipole layers and surface charge layers along the pore mouth-water interface can have on the electrical properties of a transmembrane channel. Three specific molecular sources are considered: dipole layers formed by membrane phospholipids, dipole layers lining the mouth of a channel-forming protein, and charged groups in the mouth of a channel-forming protein. We find, consistent with previous work, that changing the lipid-water potential difference only influences channel conduction if the rate-limiting step takes place well inside the channel constriction. We find that either mouth dipoles or mouth charges can act as powerful ion attractors increasing either cation or anion concentration near the channel entrance to many times its bulk value, especially at low ionic strengths. The effects are sufficient to reconcile the apparently contradictory properties of high selectivity and high conductivity, observed for a number of K+ channel systems. We find that localizing the electrical sources closer to the constriction entrance substantially increases their effectiveness as ion attractors; this phenomenon is especially marked for dipolar distributions. An approximate treatment of electrolyte shielding is used to discriminate between the various mechanisms for increasing ionic concentration near the constriction entrance. Dipolar potentials are far less sensitive to ionic strength variation than potentials due to fixed charges. We suggest that the K+ channel from sarcoplasmic reticulum does not have a fixed negative charge near the constriction entrance; we suggest further that the Ca+2-activated K+ channel from transverse tubule does have such a charge.

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.