We investigated the effects of substituting two of the four tryptophans (the “inner pair” Trp9,11 or the “outer pair” Trp13,15) in gramicidin A (gA) channels. The conformational preferences of the double-substituted gA analogues were assessed using circular dichroism spectroscopy and size-exclusion chromatography, which show that the inner tryptophans 9 and 11 are critical for the gA’s conformational preference in lipid bilayer membranes. [Phe13,15]gA largely retains the single-stranded helical channel structure, whereas of [Phe9,11]gA exists primarily as double-stranded conformers. Within this context, the 2H-NMR spectra from labeled tryptophans were used to examine the changes in average indole ring orientations, induced by the Phe substitutions and by the shift in conformational preference. Using a method for deuterium labeling of already synthesized gAs, we introduced deuterium selectively onto positions C2 and C5 of the remaining tryptophan indole rings in the substituted gA analogues for solid-state 2H-NMR spectroscopy. The (least possible) changes in orientation and overall motion of each indole ring were estimated from the experimental spectra. Regardless of the mixture of backbone folds, the indole ring orientations observed in the analogues are similar to those found previously for gA channels. Both Phe-substituted analogues form single-stranded channels, as judged from the formation of heterodimeric channels with the native gA. [Phe13,15]gA channels have Na+ currents that are ~50% and lifetimes ~80% those of native gA channels. The double-stranded conformer(s) of [Phe9,11]gA do not form detectable channels. The minor single-stranded population of [Phe9,11]gA forms channels with Na+ currents that are ~25% and single-channel lifetimes that are ~300% those of native gA channels. Our results suggest that Trp9 and Trp11, when “reaching” for the interface, tend to drive both monomer folding (to “open” a channel) and dimer dissociation (to “close” a channel). Furthermore, the dipoles of Trp9 and Trp11 are relatively more important for the single-channel conductance than are the dipoles of Trp13 and Trp15.

Linear rate-equilibrium (RE) relations, also known as linear free energy relations, are widely observed in chemical reactions, including protein folding, enzymatic catalysis, and channel gating. Despite the widespread occurrence of linear RE relations, the principles underlying the linear relation between changes in activation and equilibrium energy in macromolecular reactions remain enigmatic. When examining amphiphile regulation of gramicidin channel gating in lipid bilayers, we noted that the gating process could be described by a linear RE relation with a simple geometric interpretation. This description is possible because the gating process provides a well-understood reaction, in which structural changes in a bilayer-embedded model protein can be studied at the singlemolecule level. It is thus possible to obtain quantitative information about the energetics of the reaction transition state and its position on a spatial coordinate. It turns out that the linear RE relation for the gramicidin monomer-dimer reaction can be understood, and the quantitative relation between changes in activation energy and equilibrium energy can be interpreted, by considering the effects of amphiphiles on the changes in bilayer elastic energy associated with channel gating. We are not aware that a similar simple mechanistic explanation of a linear RE relation has been provided for a chemical reaction in a macromolecule. RE relations generally should be useful for examining how amphiphile-induced changes in bilayer properties modulate membrane protein folding and function, and for distinguishing between direct (e.g., due to binding) and indirect (bilayer-mediated) effects.Brønsted | linear free energy relationships | phi value | bilayer elasticity I t is a common observation that manipulations that alter the energetics of a reaction:alter the rate constants (k 1 and k −1 ) and equilibrium constant (K eq ¼ k 1 ∕k −1 ), such that lnfk 1 g is a linear function of lnfK eq g. This linearity is interpreted to mean that, for a series of manipulations of the reaction, the activation free energy (ΔG ‡ ) varies as a linear function of the equilibrium free energy (ΔG 0 ):where a is a slope factor and b a constant (1-3). Such linear relations, known as linear rate-equilibrium (RE) relations (4), linear free energy relations (5), or linear rate-equilibrium free energy relations (6), have been observed and studied since the early 1900s. First observed in acid-based reactions (7-9), they have been identified in a wide range of reactions (1-3). Leffler proposed, based on studies of covalent reactions, that the slope factor a (Eq. 2) identifies the position of the transition state on a reaction coordinate, where S and P are positioned at 0 and 1, respectively (5). Marcus and coworkers deduced the principles underlying linear RE relations in electron transfer processes using a model in which the transfer is described as a one-step transition between two harmonic energy wells (10, 11). Fersht and coworkers used linear RE relations associated with p...

The canonical mechanism of gramicidin (gA) channel formation is transmembrane dimerization of nonconducting subunits that reside in opposite bilayer leaflets. The channels do not open and close; they appear and disappear due to subunit association and dissociation. Many different types of experiments support this monomer ↔ dimer mechanism. Recently, however, this mechanism was challenged, based on experiments with lipid vesicle-incorporated gA under conditions where vesicle fusion could be controlled. In these experiments, sustained channel activity was observed long after fusion had been terminated, which led to the proposal that gA single-channel current transitions result from closed-open transitions in long-lived bilayer-spanning dimers. This proposal is at odds with 40 years of experiments, but involves the key assumption that gA monomers do not exchange between bilayers. We tested the possibility of peptide exchange between bilayers using three different types of experiments. First, we demonstrated the exchange of gA between 1,2-dierucoyl-sn-glycero-3-phosphocholine (DCPC) or 1,2-dioleoyl-sn-glycero-3-phosphocholine (DCPC) lipid vesicles using a fluorescence assay for gA channel activity. Second, we added gA-free DCPC vesicles to both sides of planar DCPC bilayers preincubated with gA, which reduced channel activity up to 10-fold. Third, we added gA-containing DCPC vesicles to one or both sides of DCPC planar bilayers, which produced much higher channel activity when the gA-containing vesicles were added to both sides of the bilayer, as compared to one side only. All three types of experiments show that gA subunits can exchange between lipid bilayers. The exchange of subunits between bilayers thus is firmly established, which becomes a crucial consideration with respect to the mechanism of channel formation.

The canonical mechanism of gramicidin (gA) channel formation is a transmembrane dimerization of non-conducting subunits that reside in opposite bilayer leaflets. The channels do not open and close per se; rather they appear and disappear. This basic monomer-dimer mechanism is supported by conductanceconcentration studies, fluorescence measurements, conductance relaxation experiments using voltage, and pressure and light-inactivation experiments to perturb the monomer-dimer equilibrium. Recently this mechanism was challenged by Jones et al. (BJ 98:1486, 2010). Using lipid vesicle-incorporated gA under conditions where vesicle fusion could be controlled, Jones et al. proposed that gA single-channel current transitions result from closed-open transitions in long-lived bilayer-spanning dimers. A key assumption in these experiments is that gA monomers do not partition between vesicles; see

Laurdan and di-4-ANEPPDHQ are membrane order reporting probes whose peak emission wavelengths depend on the lipid environment. The probes report membrane order through different mechanisms, laurdan by sensing changes in the level of water penetration into the lipid bilayer and Di-4-ANEPPDHQ by sensing dipole potential changes in the membrane. Laurdan and di-4-ANEPPDHQ are excited by UV and blue light, respectively, and both show an ~50 nm blue shift in emission for membranes in liquid-ordered (l o ) phase versus membranes in liquid-disordered (l d ) phase. Large unilamelar vesicles (LUVs) in l o phase were created by mixing sphingomyelin, DOPC spiked with 5% DPPG and cholesterol in 1:1:2 ratio. LUVs in l d phase were created only using DOPC spiked with 5% DPPG. Transmembrane polypeptides, mastoparan (a 14-residue peptide toxin isolated from wasp venom) or bovine prion protein (N-terminal residues 1-30), were added to 100 nm LUVs stained with 1mM laurdan or di-4-ANEPPDHQ in up to 1:10 protein/total lipid ratio. The laurdan and the di-4-ANEPPDHQ emission spectra were measured for both l o and l d phase LUVs before and after the addition of polypeptides and remained unchanged for all conditions. The integrity and size distribution of the LUVs upon addition of the polypeptides were determined by dynamic laser light scattering and no changes were detected. The insertion efficiency of the polypeptides into LUVs was determined by measuring their 3D polypeptide structure by circular dichroism. Both polypeptides had an alpha helical conformation compatible with them being inserted into the lipid bilayer. Our results suggest that the presence of proteins in biological membranes does not influence the spectra of laurdan and di-4-ANEPPDHQ showing that the dyes report solely on lipid order.