Structure of an isolated gramicidin A double helical species by high-resolution nuclear magnetic resonance

Alignment of lyotropic liquid crystals using magnetic nanoparticles improves ionic transport through built-in peptide ion channels

HYPOTHESIS

We hypothesize that simultaneous incorporation of ion channel peptides (in this case, potassium channel as a model) and hydrophobic magnetite Fe3O4 nanoparticles (hFe3O4NPs) within lipidic hexagonal mesophases, and aligning them using an external magnetic field can significantly enhance ion transport through lipid membranes.

EXPERIMENTS

In this study, we successfully characterized the incorporation of gramicidin membrane ion channels and hFe3O4NPs in the lipidic hexagonal structure using SAXS and cryo-TEM methods. Additionally, we thoroughly investigated the conductive characteristics of freestanding films of lipidic hexagonal mesophases, both with and without gramicidin potassium channels, utilizing a range of electrochemical techniques, including impedance spectroscopy, normal pulse voltammetry, and chronoamperometry.

FINDINGS

Our research reveals a state-of-the-art breakthrough in enhancing ion transport in lyotropic liquid crystals as matrices for integral proteins and peptides. We demonstrate the remarkable efficacy of membranes composed of hexagonal lipid mesophases embedded with K+ transporting peptides. This enhancement is achieved through doping with hFe3O4NPs and exposure to a magnetic field. We investigate the intricate interplay between the conductive properties of the lipidic hexagonal structure, hFe3O4NPs, gramicidin incorporation, and the influence of Ca2+ on K+ channels. Furthermore, our study unveils a new direction in ion channel studies and biomimetic membrane investigations, presenting a versatile model for biomimetic membranes with unprecedented ion transport capabilities under an appropriately oriented magnetic field. These findings hold promise for advancing membrane technology and various biotechnological and biomedical applications of membrane proteins.

Effects of Calcium Ions on the Antimicrobial Activity of Gramicidin A

Gramicidin A (gA) is a linear antimicrobial peptide that can form a channel and specifically conduct monovalent cations such as H+ across the lipid membrane. The antimicrobial activity of gA is associated with the formation of hydroxyl free radicals and the imbalance of NADH metabolism, possibly a consequence caused by the conductance of cations. The ion conductivity of gramicidin A can be blocked by Ca2+ ions. However, the effect of Ca2+ ions on the antimicrobial activity of gA is unclear. To unveil the role of Ca2+ ions, we examined the effect of Ca2+ ions on the antimicrobial activity of gramicidin A against Staphylococcus aureus (S. aureus). Results showed that the antimicrobial mechanism of gA and antimicrobial activity by Ca2+ ions are concentration-dependent. At the low gA concentration (≤1 μM), the antimicrobial mechanism of gA is mainly associated with the hydroxyl free radical formation and NADH metabolic imbalance. Under this mode, Ca2+ ions can significantly inhibit the hydroxyl free radical formation and NADH metabolic imbalance. On the other hand, at high gA concentration (≥5 μM), gramicidin A acts more likely as a detergent. Gramicidin A not only causes an increase in hydroxyl free radical levels and NAD+/NADH ratios but also induces the destruction of the lipid membrane composition. At this condition, Ca2+ ions can no longer reduce the gA antimicrobial activity but rather enhance the bacterial killing ability of gramicidin A.

The Effect of Calcium and Halide Ions on the Gramicidin A Molecular State and Antimicrobial Activity

Gramicidin A (gA) forms several convertible conformations in different environments. In this study, we investigated the effect of calcium halides on the molecular state and antimicrobial activity of gramicidin A. The molecular state of gramicidin A is highly affected by the concentration of calcium salt and the type of halide anion. Gramicidin A can exist in two states that can be characterized by circular dichroism (CD), mass, nuclear magnetic resonance (NMR) and fluorescence spectroscopy. In State 1, the main molecular state of gramicidin A is as a dimer, and the addition of calcium salt can convert a mixture of four species into a single species, which is possibly a left-handed parallel double helix. In State 2, the addition of calcium halides drives gramicidin A dissociation and denaturation from a structured dimer into a rapid equilibrium of structured/unstructured monomer. We found that the abilities of dissociation and denaturation were highly dependent on the type of halide anion. The dissociation ability of calcium halides may play a vital role in the antimicrobial activity, as the structured monomeric form had the highest antimicrobial activity. Herein, our study demonstrated that the molecular state was correlated with the antimicrobial activity.

An experimental study of the solvent-dependent self-assembly/disassembly and conformer preferences of gramicidin A

The solvent dependence of self-assembly/disassembly kinetics and conformer preferences of the gramicidin A (GA) dimer is investigated using a combination of techniques, viz., electrospray ionization-ion mobility-mass spectrometry (IM-MS), collision-induced dissociation (CID), and hydrogen/deuterium exchange (HDX)-MS. IM-MS measurements reveal that there are possibly three distinct GA dimeric species, detected as sodium ion adduct ions [2GA + 2Na](2+), and these are assigned as the parallel β-helix, antiparallel β-helix, and head-to-head dimer. The monomerization kinetics and equilibrium abundances of the dimer ions depend upon solvent polarity. The antiparallel β-helix was the thermodynamically preferred species in less polar solvents. HDX measurements and collision-induced dissociation (CID) of the intermediate complex confirm the well-protected dimer geometry with strong intermolecular hydrogen bonds. This combined IM-HDX-CID methodology provides a comprehensive view of GA self-assembly/disassembly in low dielectric solutions, showing its potential utility in solving solution-phase protein self-assembly/disassembly kinetics and providing structural information of the multimers at the same time.

Channel and nonchannel forms of spin-labeled gramicidin in membranes and their equilibria

Channel and nonchannel forms of gramicidin A (GA) were studied by ESR in various lipid environments using new mono- and double-spin-labeled compounds. For GA channels, we demonstrate here how pulse dipolar ESR can be used to determine the orientation of the membrane-traversing molecule relative to the membrane normal and to study subtle effects of lipid environment on the interspin distance in the spin-labeled gramicidin channel. To study nonchannel forms of gramicidin, pulse dipolar ESR was used first to determine interspin distances corresponding to monomers and double-helical dimers of spin-labeled GA molecules in the organic solvents trifluoroethanol and octanol. The same distances were then observed in membranes. Since detection of nonchannel forms in the membrane is complicated by aggregation, we suppressed any dipolar spectra from intermolecular interspin distances arising from the aggregates by using double-labeled GA in a mixture with excess unlabeled GA. In hydrophobic mismatching lipids (L(β) phase of DPPC), gramicidin channels dissociate into free monomers. The backbone structure of the monomeric form is similar to a monomeric unit of the channel dimer. In addition to channels and monomers, the double-helical conformation of gramicidin is present in some membrane environments. In the gel phase of saturated phosphatidylcholines, the fraction of double helices increases in the following order: DLPC < DMPC < DSPC < DPPC. The equilibrium DHD/monomer ratio in DPPC was determined. In membranes, the double-helical form is present only in aggregates. In addition, we studied the effect of N-terminal substitution in the GA molecule upon channel formation. This work demonstrates how pulsed dipolar ESR may be utilized to study complex equilibria of peptides in membranes.

250GHz CW gyrotron oscillator for dynamic nuclear polarization in biological solid state NMR

In this paper, we describe a 250 GHz gyrotron oscillator, a critical component of an integrated system for magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments at 9T, corresponding to 380 MHz (1)H frequency. The 250 GHz gyrotron is the first gyro-device designed with the goal of seamless integration with an NMR spectrometer for routine DNP enhanced NMR spectroscopy and has operated under computer control for periods of up to 21 days with a 100% duty cycle. Following a brief historical review of the field, we present studies of the membrane protein bacteriorhodopsin (bR) using DNP enhanced multidimensional NMR. These results include assignment of active site resonances in [U-(13)C, (15)N]-bR and demonstrate the utility of DNP for studies of membrane proteins. Next, we review the theory of gyro-devices from quantum mechanical and classical viewpoints and discuss the unique considerations that apply to gyrotron oscillators designed for DNP experiments. We then characterize the operation of the 250 GHz gyrotron in detail, including its long-term stability and controllability. We have measured the spectral purity of the gyrotron emission using both homodyne and heterodyne techniques. Radiation intensity patterns from the corrugated waveguide that delivers power to the NMR probe were measured using two new techniques to confirm pure mode content: a thermometric approach based on the temperature-dependent color of liquid crystalline media applied to a substrate and imaging with a pyroelectric camera. We next present a detailed study of the mode excitation characteristics of the gyrotron. Exploration of the operating characteristics of several fundamental modes reveals broadband continuous frequency tuning of up to 1.8 GHz as a function of the magnetic field alone, a feature that may be exploited in future tunable gyrotron designs. Oscillation of the 250 GHz gyrotron at the second harmonic of cyclotron resonance begins at extremely low beam currents (as low 12 mA) at frequencies between 320 and 365 GHz, suggesting an efficient route for the generation of even higher frequency radiation. The low starting currents were attributed to an elevated cavity Q, which is confirmed by cavity thermal load measurements. We conclude with an appendix containing a detailed description of the control system that safely automates all aspects of the gyrotron operation.

Direct analysis of gramicidin double helices using packed column supercritical fluid chromatography

Direct analysis of the monomeric and four double helical dimeric conformations of gramicidin has been achieved using packed column supercritical fluid chromatography (pSFC). Using a PRP-1 polymeric column and typical conditions of 40 degrees C column temperature, 25 MPa column pressure, and 35% n-pentanol modifier addition, all of the gramicidin conformers were readily separated. To evaluate the method, the dynamic characteristics of the monomer and dimer species were monitored as a function of solvent type, incubation time, solvent temperature, and initial concentration. The findings agree with those previously obtained by other methods but also yield new information about the relative amounts of two closely related dimers (species 1 and 2) as well as the simultaneous changes in the full dimer/monomer distribution. Results indicate that the developed pSFC method can be an informative complimentary tool for readily monitoring changes in the full profile of gramicidin species present in different environments.

Structural restraints and heterogeneous orientation of the gramicidin A channel closed state in lipid bilayers

Although there have been several decades of literature illustrating the opening and closing of the monovalent cation selective gramicidin A channel through single channel conductance, the closed conformation has remained poorly characterized. In sharp contrast, the open-state dimer is one of the highest resolution structures yet characterized in a lipid environment. To shift the open/closed equilibrium dramatically toward the closed state, a lower peptide/lipid molar ratio and, most importantly, long-chain lipids have been used. For the first time, structural evidence for a monomeric state has been observed for the native gramicidin A peptide. Solid-state NMR spectroscopy of single-site (15)N-labeled gramicidin in uniformly aligned bilayers in the L(alpha) phase have been observed. The results suggest a kinked structure with considerable orientational heterogeneity. The C-terminal domain is well structured, has a well-defined orientation in the bilayer, and appears to be in the bilayer interfacial region. On the other hand, the N-terminal domain, although appearing to be well structured and in the hydrophobic core of the bilayer, has a broad range of orientations relative to the bilayer normal. The structure is not just half of the open-state dimer, and neither is the structure restricted to the surface of the bilayer. Consequently, the monomeric or closed state appears to be a hybrid of these two models from the literature.

Electrospray ionization-mass spectrometry and tandem mass spectrometry reveal self-association and metal-ion binding of hydrophobic peptides: a study of the gramicidin dimer

Gramicidin is a membrane pentadecapeptide that acts as a channel, allowing the passage of monovalent metal ions and assisting in bacterial cell death. The active form is a noncovalently bound dimer. One means to study the self-assembly of this peptide has been to compare the state of the peptide in various solvents ranging from hydrophilic (e.g., trifluoroethanol) to hydrophobic (e.g., n-propanol). In this article, we report the use of electrospray mass spectrometry to study the self-association of gramicidin in various organic and mixed solvents that are introduced directly into the mass spectrometer. The dimer (both homo and hetero) can survive the introduction into the gas phase, and the amount in the gas phase increases with the decreasing dielectric constant of the solvent, reflecting solution-phase behavior. Tandem mass spectrometry data reveal that the stability of dimer in the gas phase decreases with increasing metal ion size, strongly suggesting that the metal ion binds inside the dimer between the monomers.

Gramicidin A and its complexes with Cs+ and Tl+ ions in organic solvents. A study by steady state and time resolved emission spectroscopy

Gramicidin A (gr A), a linear pentadecapeptide containing four trp residues has been studied using steady state and time resolved fluorescence (at 298 K) and phosphorescence (at 77 K) in methanol (CH3OH), ethanol (C2H5OH), dimethyl sulfoxide (DMSO), 1,4-dioxane, 2-methyl tetrahydrofuran (2-MeTHF), ethanol/benzene (C2H5OH/C6H6) mixed solvent. Similar studies have also been carried out in CH3OH containing monovalent cations K+, Cs+, Tl+ and divalent cation Ca2+. Lambda(max) of fluorescence is found to be a good signature of the different forms having double helical structure [dh (1) to dh (4)] (J. Struct. Biol. 121 (1998) 123-141). Steady state and time resolved quenching studies of gr A by KI in CH3OH and DMSO and life time of the emitting singlet states of gr A support that gr A exists as a mixture of different forms of double helical (dh) structure [dh (1) to dh (4)] in CH3OH and as a random coil structure in DMSO. This study further indicates that emitting trp residue in DMSO is better shielded than that in CH3OH. Phosphorescence spectra of gr A at 77 K in CH3OH glass suggests that gr A retains a particular conformation dh (3) in this matrix. The phosphorescence spectra of gr A [conformation dh (4)] in 2-MeTHF at 77 K is further red shifted indicating that among all the dh forms, dh (4) has the emitting trp residue in most hydrophobic environment. The hydrophobicity of the emitting tryptophan environment is thus found to be in the order: dh (1)<dh (3)<dh (4). Since 2-MeTHF forms a clear glass at low temperature, it is thus possible to study the side chain arrangement of gr A dh (4) as a function of temperature. The phosphorescence spectra in different alcohol glassy matrix are in conformity with the observation of different side chain arrangement of gr A as one changes the polarity of alcohol. Steady state and time resolved quenching studies of gr A using Cs+ ion in CH3OH at 298 K clearly demonstrate the two binding sites for the metal ions and provide the value of equilibrium constant of the 'non-emitting' complex of gr A with Cs+ ion in the ground state. The observation of distinct red shift of the (0,0) band of the phosphorescence spectra of the complexes of gr A with K+, Cs+ and Tl+ ions at 77 K compared to that in CH3OH glass confirms the metal ion induced change of conformation in dh (3). The result also suggests that the emitting trp residues in the complexes are in somewhat more hydrophobic environment compared with that in the free gr A in CH3OH glass. The triplet state life time of these complexes indicate that the heavy metal ions Cs+ and Tl+ are within a Van der Waal's distance of emitting trp residue in gr A in CH3OH glass at 77 K so that they are capable of inducing increased spin-orbit coupling due to a heavy atom effect.

Common structural features in gramicidin and other ion channels

This review compares and contrasts the structures of several different types of ion channels with known three-dimensional structures, including gramicidin and the family of peptaibol channels, as well as the Streptomyces lividans potassium channel, to reveal common features in their structures that relate to their functional roles in ion binding and transport across membranes. Specifically, the locations of aromatic amino acids, the dimensions of the molecules, the multimeric nature of the channels and the roles of hydrogen bonds in stabilising such structures, the means by which the channels open and close, and the chemical nature of the groups which make up the channel lumen are discussed. The emphasis is on the commonality of features found in model channels, which may ultimately be found in other biological channel structures.

Solvent effects on the conformation of the transmembrane peptide gramicidin A: insights from electrospray ionization mass spectrometry

The binding of sodium ions to the transmembrane channel peptide gramicidin A has permitted the use of electrospray ionization mass spectrometry to study its conformation in different solvent environments. The mass spectra of the peptide in the various solvents suggest that different conformations of gramicidin A differ in their ability to bind metal ions. The data are consistent with monomeric behavior of gramicidin A in trifluoroethanol and dimethyl sulfoxide solutions, but reveal the presence of noncovalent intermolecular interactions in ethanol solution through the observation of heterodimers formed between the naturally occurring variants of the peptide. The addition of 50% v/v of water to the ethanolic solution causes changes in the circular dichroism spectrum of the peptide, suggestive of a shift in the equilibrium mixture of conformers present toward monomeric species, a result supported by its mass spectrum. The structure of gramicidin A in trifluoroethanol has also been investigated by hydrogen exchange measurements monitored by mass spectrometry. The observation of significant protection against exchange suggests that the monomeric peptide is highly structured in trifluoroethanol. The results indicate that mass spectrometry has the potential to probe the conformational behavior of neutral hydrophobic peptides in environments that mimic their functional states.

Water: foldase activity in catalyzing polypeptide conformational rearrangements

Polypeptide conformer interconversion in a low dielectric environment is shown to be highly dependent on water concentration. Water increases this rate by 10(3), apparently by catalyzing hydrogen bond exchange, and thereby presenting functional properties analogous to that of a foldase. This catalytic effect is demonstrated on the interconversion of a parallel gramicidin dimer into an antiparallel dimer. A Hill coefficient of 6.5 is observed, illustrating the highly cooperative nature of the process. Protein folding in nonpolar environs, such as the hydrophobic core of a protein or the hydrophobic domain of a lipid bilayer, may be contingent on and rate-limited by the scarcity of water.

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

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-A 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 reflect 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. Contrary to a recent claim [Burkhart, B. M., Li, N., Langs, D. A., Pangborn, W. A. & Duax, W. L. (1998) Proc. Natl. Acad. Sci. USA 95, 12950-12955], the solid-state NMR constraints for gramicidin A in a lipid bilayer are not consistent with an x-ray crystallographic structure for gramicidin having a double-stranded, right-handed helix with 7.2 residues per turn.

Solid-state NMR and hydrogen-deuterium exchange in a bilayer-solubilized peptide: structural and mechanistic implications

Hydrogen-deuterium exchange has been monitored by solid-state NMR to investigate the structure of gramicidin M in a lipid bilayer and to investigate the mechanisms for polypeptide insertion into a lipid bilayer. Through exchange it is possible to observe 15N-2H dipolar interactions in oriented samples that yield precise structural constraints. In separate experiments the pulse sequence SFAM was used to measure dipolar distances in this structure, showing that the dimer is antiparallel. The combined use of orientational and distance constraints is shown to be a powerful structural approach. By monitoring the hydrogen-deuterium exchange at different stages in the insertion of peptides into a bilayer environment it is shown that dimeric gramicidin is inserted into the bilayer intact, i.e., without separating into monomer units. The exchange mechanism is investigated for various sites and support for a relayed imidic acid mechanism is presented. Both acid and base catalyzed mechanisms may be operable. The nonexchangeable sites clearly define a central core to which water is inaccessible or hydroxide or hydronium ion is not even momentarily stable. This provides strong evidence that this is a nonconducting state.

Recent Advances in the High Resolution Structures of Bacterial Channels: Gramicidin A

Gramicidin is a polypeptide antibiotic which forms dimeric channels specific for the transport of monovalent cations across membranes. It adopts several different conformations, most notably double helical (pore) and helical dimer (channels) forms, which have very different structural and functional characteristics. This review focuses on recent high resolution structure determinations of both the pore and channel forms of the molecule by X-ray crystallographic and/or NMR spectroscopic techniques. It discusses the structural consequences of binding ions and the location of ion binding sites and how the structures are related to the conductance properties of the molecule. This relatively simple molecule is probably the best characterized ion channel (both structurally and functionally) and has, to date, been the principal proving-ground for many of our ideas about the molecular nature of ion conduction in membranes. Copyright 1998 Academic Press.

High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints

BACKGROUND

Solid-state nuclear magnetic resonance (NMR) spectroscopy provides novel structural constraints from uniformly aligned samples. These orientational constraints orient specific atomic sites with respect to the magnetic field direction and the unique molecular axis of alignment. Solid-state NMR is uniquely and ideally suited for providing such structural constraints on polypeptides and proteins in a lamellar phase lipid environment. Membrane protein structure represents a great challenge for structural biologists; a new approach for characterizing high resolution three-dimensional structure in such an environment is needed.

RESULTS

The optimal use of orientational constraints for defining three-dimensional structures is demonstrated with the elucidation of the gramicidin A channel structure at high resolution. Initial structures are refined against both the experimental constraints and the CHARMM energy using a novel simulated-annealing protocol to define torsion angle solutions with an error bar of approximately +/- 5 degrees.

CONCLUSIONS

This analysis results in the determination of a high-resolution, time averaged structure of gramicidin A obtained in a lipid bilayer environment above the gel-to-liquid crystalline phase transition temperature. It is demonstrated that solid-state NMR can be used to establish polypeptide, and potentially protein, structures in such an environment. Furthermore, this high-resolution structure is demonstrated to provide new insights into polypeptide function. For the gramicidin A channel the roles of the indole groups that facilitate ion transport and details of the cation solvation environment provided by the amide oxygens are characterized.

Solvent effects on the conformation and far UV CD spectra of gramicidin

Solvent effects on the far-uv CD spectra of the polypeptide gramicidin have been studied systematically in a series of alcohols of increasing chain length, ranging from methanol to dodecanol. The effects observed are of two types: primary, involving a change in the equilibrium mixture of conformers present, and secondary, involving a shift in the spectral peak positions as a function of solvent polarizability. To quantitate the primary effect, the ratio of the individual conformers present was estimated by deconvolution of the spectra into their component species. For short chain length alcohols, both parallel and antiparallel double helices are found in considerable abundance. As the solvent chain length is increased and its polarity is decreased, the left-handed antiparallel double helical species is favored. For all alcohols with chain lengths of four or more carbon atoms, the ratio of the conformers present remains relatively constant. To quantitatively examine the secondary effect, the magnitudes of the spectral shifts on the dominant conformer (species 3) have been correlated with the dielectric constants and refractive indices of the solvents, thereby indicating what underlying physical properties are responsible for these shifts. This work thus demonstrates that for gramicidin, a flexible polypeptide, the solvent effects on the CD spectra can be resolved into two types: changes due to the mixture of conformers present and shifts in the spectral characteristics. Both effects need to be considered when interpreting CD spectra in terms of secondary structure for this and other polypeptides in nonaqueous solutions.

Membrane structure and dynamics as viewed by solid-state NMR spectroscopy

The purpose of the present study is the investigation of the structure and dynamics of biological membranes using solid-state nuclear magnetic resonance (NMR) spectroscopy. Two approaches are used in our laboratory. The first involves the measurement of high-resolution 13C and 1H spectra obtained by the magic angle spinning (MAS) technique while the second approach involves the measurement of 31P and 2H powder spectra in static samples. This paper will present some recent results obtained by high-resolution solid-state 1H NMR on the conformation of gramicidin A incorporated in a phosphatidylcholine bilayers. More specifically, we were able to observe changes in the gramicidin spectra as a function of the cosolubilization solvent initially used to prepare the samples. The interaction between lipid bilayers and an anticancer drug derived from chloroethylurea was also investigated using proton NMR spectroscopy. Finally, we have studied the interaction between cardiotoxin, a toxic protein extracted from snake venom, and negatively charged lipid bilayers using 31P solid-state NMR spectroscopy.

Gramicidin channels in phospholipid bilayers with unsaturated acyl chains

In organic solvents gramicidin A (gA) occurs as a mixture of slowly interconverting double-stranded dimers. Membrane-spanning gA channels, in contrast, are almost exclusively single-stranded beta(6,3)-helical dimers. Based on spectroscopic evidence, it has previously been concluded that the conformational preference of gA in phospholipid bilayers varies as a function of the degree of unsaturation of the acyl chains. Double-stranded pi pi(5,6)-helical dimers predominate (over single-stranded beta(6,3)-helical dimers) in lipid bilayer membranes with polyunsaturated acyl chains. We therefore examined the characteristics of channels formed by gA in 1-palmitoyl-2-oleoylphosphatidylcholine/n-decane, 1,2-dioleoylphosphatidylcholine/n-decane, and 1,2-dilinoleoylphosphatidylcholine/n-decane bilayers. We did not observe long-lived channels that could be conducting double-stranded pi pi(5,6)-helical dimers in any of these different membrane environments. We conclude that the single-stranded beta(6,3)-helical dimer is the only conducting species in these bilayers. Somewhat surprisingly, the average channel duration and channel-forming potency of gA are increased in dilinoleoylphosphatidylcholine/n-decane bilayers compared to 1-palmitoyl-2-oleoylphosphatidylcholine/n-decane and dioleoylphosphatidylcholine/n-decane bilayers. To test for specific interactions between the aromatic side chains of gA and the acyl chains of the bilayer, we examined the properties of channels formed by gramicidin analogues in which the four tryptophan residues were replaced with naphthylalanine (gN), tyrosine (gT), and phenylalanine (gM). The results show that all of these analogue channels experience the same relative stabilization when going from dioleoylphosphatidylcholine to dilinoleoylphosphatidylcholine bilayers.

Protein stability and conformational rearrangements in lipid bilayers: linear gramicidin, a model system

The replacement of four tryptophans in gramicidin A by four phenylalanines (gramicidin M) causes no change in the molecular fold of this dimeric peptide in a low dielectric isotropic organic solvent, but the molecular folds are dramatically different in a lipid bilayer environment. The indoles of gramicidin A interact with the anisotropic bilayer environment to induce a change in the molecular fold. The double-helical fold of gramicidin M, as opposed to the single-stranded structure of gramicidin A, is not compatible with ion conductance. Gramicidin A/gramicidin M hybrid structures have also been prepared, and like gramicidin M homodimers, these dimeric hybrids appear to have a double-helical fold, suggesting that a couple of indoles are being buried in the bilayer interstices. To achieve this equilibrium structure (i.e., minimum energy conformation), incubation at 68 degrees C for 2 days is required. Kinetically trapped metastable structures may be more common in lipid bilayers than in an aqueous isotropic environment. Structural characterizations in the bilayers were achieved with solid-state NMR-derived orientational constraints from uniformly aligned lipid bilayer samples, and characterizations in organic solvents were accomplished by solution NMR.

Conformational trapping in a membrane environment: a regulatory mechanism for protein activity?

Functional regulation of proteins is central to living organisms. Here it is shown that a nonfunctional conformational state of a polypeptide can be kinetically trapped in a lipid bilayer environment. This state is a metastable structure that is stable for weeks just above the phase transition temperature of the lipid. When the samples are incubated for several days at 68 degrees C, 50% of the trapped conformation converts to the minimum-energy functional state. This result suggests the possibility that another mechanism for functional regulation of protein activity may be available for membrane proteins: that cells may insert proteins into membranes in inactive states pending the biological demand for protein function.

High resolution 1H nuclear magnetic resonance of a transmembrane peptide

Although the strong 1H-1H dipolar interaction is known to result in severe homogeneous broadening of the 1H nuclear magnetic resonance (NMR) spectra of ordered systems, in the fluid phase of biological and model membranes the rapid, axially symmetric reorientation of the molecules about the local bilayer normal projects the dipolar interaction onto the motional symmetry axis. Because the linewidth then scales as (3 cos2 theta-1)/2, where theta is the angle between the local bilayer normal and the magnetic field, the dipolar broadening has been reduced to an "inhomogeneous" broadening by the rapid axial reorientation. It is then possible to obtain high resolution 1H-NMR spectra of membrane components by using magic angle spinning (MAS). Although the rapid axial reorientation effectively eliminates the homogeneous dipolar broadening, including that due to n = 0 rotational resonances, the linewidths observed in both lipids and peptides are dominated by low frequency motions. For small peptides the most likely slow motions are either a "wobble" or reorientation of the molecular diffusion axis relative to the local bilayer normal, or the reorientation of the local bilayer normal itself through surface undulations or lateral diffusion over the curved surface. These motions render the peptide 1H-NMR lines too broad to be observed at low spinning speeds. However, the linewidths due to these slow motions are very sensitive to spinning rate, so that at higher speeds the lines become readily visible. The synthetic amphiphilic peptide K2GL20K2A-amide (peptide-20) has been incorporated into bilayers of 1,2-di-d 27-myristoyl-sn-glycero-3-phosphocholine (DMPC-d54) and studied by high speed 1H-MAS-NMR. The linewidths observed for this transbilayer peptide, although too broad to be observable at spinning rates below -5 kHz, are reduced to 68 Hz at a spinning speed of 14 kHz (at 500C). Further improvements in spinning speed and modifications in sample composition designed to reduce the effectiveness of the slow motions responsible for the linewidth should result in significant further reduction in peptide linewidths. With this technique, there is now the potential for the use of 1H-MAS-NMR for the study of conformation, folding, and dynamics of small membrane peptides and protein fragments.

High-speed magic angle spinning solid-state 1H nuclear magnetic resonance study of the conformation of gramicidin A in lipid bilayers

One- and two-dimensional solid-state 1H nuclear magnetic resonance spectra of gramicidin A incorporated in a dimyristoylphosphatidylcholine membrane have been obtained with use of high-speed magic angle spinning. By rotating the sample at 13 kHz, it is possible to observe signals in the 1H spectra between 6.0 and 9.0 ppm attributable to the aromatic protons of the tryptophan residues and the formyl group proton of gramicidin A. Two-dimensional solid-state COSY spectra provided information for the peak assignments. Moreover, changes in the 1H spectra have been observed as a function of the co-solubilization solvent initially used to prepare the samples and therefore as a function of the conformation adopted by gramicidin A. Three organic solvents have been used: trifluoroethanol, a mixture of methanol/chloroform (1:1 v/v), and ethanol. The conformational interconversion of gramicidin A from the double helix conformation to the channel structure for the sample prepared from ethanol was confirmed by following the time evolution of the proton spectra.

Conformation states of gramicidin A along the pathway to the formation of channels in model membranes determined by 2D NMR and circular dichroism spectroscopy

Gramicidin A incorporated into SDS (sodium dodecyl sulfate) micelles exists as a right-handed, N-to-N-terminal beta 6.3 helical dimer [Lomize, A. L., Orechov, V. Yu., & Arseniev, A.S. (1992) Bioorg. Khim. 18, 182-189]. In the incorporation procedure to achieve the ion channel state of gramicidin A in SDS micelles, trifluoroethanol (TFE) is used to solubilize the hydrophobic peptide before addition to the aqueous/micelle solution. The conformational transition of gramicidin A to form ion channels in SDS micelles, i.e., in TFE and 10% TFE/water, has been investigated using 2D NMR and CD spectroscopy. In neat TFE, gramicidin A was found to be monomeric and may possibly exist in an equilibrium of rapidly interconverting conformers of at least three different forms believed to be left- and/or right-handed alpha and beta 4.4 helices. It was found that the interconversion between these conformers was slowed down in 55% TFE as evident by the observation of at least three different sets of d alpha N COSY peaks although CD gave a net spectrum similar to that in neat TFE. In 10% TFE gramicidin A spontaneously forms a precipitate. The precipitated species were isolated and solubilized in dioxane where gramicidin conformers undergo very slow interconversion and could be characterized by NMR. At least seven different gramicidin A conformations were found in 10% TFE. Four of thes are the same types of double helices as previously found in ethanol (i.e., a symmetric left-handed parallel beta 5.6 double helix, an unsymmetric left-handed parallel beta 5.6 double helix, a symmetric left-handed antiparallel beta 5.6 double helix, a symmetric right-handed parallel beta 5.6 double helix); the fifth is possibly a symmetric right-handed antiparallel beta 5.6 double helix. There is also evidence for the presence of at least one form of monomeric species. Previous observation on the solvent history dependence in the ease of channel incorporation may be explained by the presence of several different folding pathways to channel formation. To test this proposal, the conformation of gramicidin A in 10% DMSO and 10% methanol was studied. In the former environment, the major form was a random coil with a minor population of double-stranded helices, while in the latter, NMR spectra indicate the presence of the same double-helical conformers as found in neat methanol.