Conformation of gramicidin A

Veatch, William R.; Fossel, Eric T.; Blout, E. R.

doi:10.1021/bi00723a001

Cited by 402 publications

(283 citation statements)

References 16 publications

(6 reference statements)

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“…Folding Preference of 1-Me-Trp gA Analogues-Gramicidin A can adopt different structural conformations depending on different solvent environments (51,59). There are two major groups of conformers with different folding patterns.…”

Section: Discussionmentioning

confidence: 99%

The Preference of Tryptophan for Membrane Interfaces

Sun

Greathouse

Andersen

et al. 2008

Journal of Biological Chemistry

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To better understand the structural and functional roles of tryptophan at the membrane/water interface in membrane proteins, we examined the structural and functional consequences of Trp 3 1-methyl-tryptophan substitutions in membranespanning gramicidin A channels. Gramicidin A channels are miniproteins that are anchored to the interface by four Trps near the C terminus of each subunit in a membrane-spanning dimer. We masked the hydrogen bonding ability of individual or multiple Trps by 1-methylation of the indole ring and examined the structural and functional changes using circular dichroism spectroscopy, size exclusion chromatography, solid state 2 H NMR spectroscopy, and single channel analysis. N-Methylation causes distinct changes in the subunit conformational preference, channel-forming propensity, single channel conductance and lifetime, and average indole ring orientations within the membrane-spanning channels. The extent of the local ring dynamic wobble does not increase, and may decrease slightly, when the indole NH is replaced by the non-hydrogen-bonding and more bulky and hydrophobic N-CH 3 group. The changes in conformational preference, which are associated with a shift in the distribution of the aromatic residues across the bilayer, are similar to those observed previously with Trp 3 Phe substitutions. We conclude that indole N-H hydrogen bonding is of major importance for the folding of gramicidin channels. The changes in ion permeability, however, are quite different for Trp 3 Phe and Trp 3 1-methyl-tryptophan substitutions, indicating that the indole dipole moment and perhaps also ring size and are important for ion permeation through these channels.

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Section: Discussionmentioning

confidence: 99%

The Preference of Tryptophan for Membrane Interfaces

Sun

Greathouse

Andersen

et al. 2008

Journal of Biological Chemistry

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“…The fact that the quantities C h 1 and g j 1 , relative to the TEO moiety, attain a maximum at less negative potentials than the quantities C h 2 and g j 2 , relative to the lipid bilayer moiety, is due to the negative dipole potential, 1 , located in the TEO moiety, which favors an incipient accumulation of K + ions on the metal side of this hydrophilic spacer as the potential is progressively shifted in the negative direction. On the other hand, the height of the potential energy barrier due to the lipid bilayer decreasing…”

Section: N′/n′′mentioning

confidence: 98%

“…φ 1 includes the dipole potential, 1 , of the hydrophilic spacer, which was estimated at about -0.250 V, negative toward the metal, on the basis of independent measurements. 34 The extrathermodynamic absolute potential difference φ t across the whole mercury|(aqueous solution) interphase is more positive than the potential E measured versus a SCE by about 0.250 V 33 .…”

Section: N′/n′′mentioning

confidence: 99%

Gramicidin Conducting Dimers in Lipid Bilayers Are Stabilized by Single-File Ionic Flux along Them

2007

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Gramicidin D was incorporated in a biomimetic membrane consisting of a lipid bilayer tethered to a mercury electrode via a hydrophilic spacer, and its behavior was investigated in aqueous 0.1 M KCl by potential-step chronocoulometry and electrochemical impedance spectroscopy. The impedance spectra, recorded from 0.1 to 1 × 10 5 Hz over a potential range of 0.7 V, were fitted to a series of RC meshes, which were related to the different substructural elements of the biomimetic membrane. These impedance spectra were compared with those obtained by incorporating valinomycin, under otherwise identical conditions. The potential dependence of the stationary currents reported on bilayer lipid membranes by Bamberg and Läuger (Bamberg, E.; Läuger, P. J. Membrane Biol. 1973, 11, 177-194) as well as those extracted from potential-step chronocoulometric measurements was interpreted by relating the increase in gramicidin dimerization to a progressive increase in single-file K + flux along the dimeric channels. An analogous approach was adopted in explaining the difference between the impedance spectra obtained with gramicidin D and those obtained with valinomycin. It is concluded that gramicidin has a low tendency to form dimers in the absence of ionic flux.

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“…In isotropic organic solvents, this peptide typically forms a doublestranded dimer that may be parallel or antiparallel, lefthanded or right-handed and has a range of residues per turn from 5.6 to 7.2 (5)(6)(7)(8)(9)(10). In the heterogeneous anisotropic lipid environment, the structure is almost exclusively singlestranded.…”

mentioning

confidence: 99%

Validation of the single-stranded channel conformation of gramicidin A by solid-state NMR

Kovacs

Quine

Cross

1999

Proc. Natl. Acad. Sci. U.S.A.

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The monovalent cation selective channel formed by a dimer of the polypeptide gramicidin A has a single-stranded, right-handed helical motif with 6.5 residues per turn forming a 4-Å diameter pore. The structure has been refined to high resolution against 120 orientational constraints obtained from samples in a liquid-crystalline phase lipid bilayer. These structural constraints from solid-state NMR ref lect the orientation of spin interaction tensors with respect to a unique molecular axis. Because these tensors are fixed in the molecular frame and because the samples are uniformly aligned with respect to the magnetic field of the NMR spectrometer, each constraint restricts the orientation of internuclear vectors with respect to the laboratory frame of reference. The structural motif of this channel has been validated, and the high-resolution structure has led to precise models for cation binding, cation selectivity, and cation conductance efficiency. The structure is consistent with the electrophysiological data and numerous biophysical studies. Orientational constraints derived from solid-state NMR can be used to determine high-resolution three-dimensional structures. Such an approach has been used to define the structure of the ion channel, gramicidin A, in lamellar phase lipids (ref. 1; PDB accession no. 1MAG). Although a reasonable model of this structure has been extant for nearly 30 years (2) and a structure was determined by solution NMR spectroscopy in SDS micelles (3, 4), crystallographic and solution NMR methods have not been successful in a lipid environment. Recently, the validity of the solid-state NMR structure has been challenged (5). In this report, the structural fold of the channel is validated by comparing predicted and observed values for structural constraints not used quantitatively in solving for the structural fold. Furthermore, the NMR observables are compared with predicted values from several structures in the Protein Data Bank. The results establish the high resolution of the solid-state structure and the clear validity of this motif in a lipid environment.Gramicidin A is a polymorphic structure and the dominant sequence in gramicidin D, the biosynthetic product from Bacillus brevis: HCO-Val-Gly-Ala-DLeu-Ala-DVal-Val-ValTrp-DLeu-Trp-DLeu-Trp-DLeu-Trp-NHCH 2 CH 2 OH. In isotropic organic solvents, this peptide typically forms a doublestranded dimer that may be parallel or antiparallel, lefthanded or right-handed and has a range of residues per turn from 5.6 to 7.2 (5-10). In the heterogeneous anisotropic lipid environment, the structure is almost exclusively singlestranded. Because of the short helix length, a single-stranded monomer buries one of its termini in the bilayer. Exposure of the carboxyl terminus to the bilayer surface and lack of exposure for the amino terminus was documented by shift reagent NMR experiments (11). It has been observed that the native monovalent cation selective channel function is maintained when formal charges are introduced at the carboxyl termin...

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Conformation of gramicidin A

Cited by 402 publications

References 16 publications

The Preference of Tryptophan for Membrane Interfaces

The Preference of Tryptophan for Membrane Interfaces

Gramicidin Conducting Dimers in Lipid Bilayers Are Stabilized by Single-File Ionic Flux along Them

Validation of the single-stranded channel conformation of gramicidin A by solid-state NMR

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