Role of terminal dipole charges in aggregation of α-helix pair in the voltage gated K+ channel

The voltage sensor domain (VSD) of the potassium ion channel KvAP is comprised of four (S1–S4) α-helix proteins, which are encompassed by several charged residues. Apart from these charges, each peptide α-helix having two inherent equal and opposite terminal dipolar charges behave like a macrodipole. The activity of voltage gated ion channel is electrostatic, where all the charges (charged residues and dipolar terminal charges) interact with each other and with the transmembrane potential. There are evidences that the role of the charged residues dominate the stabilization of the conformation and the gating process of the ion channel, but the role of the terminal dipolar charges are never considered in such analysis. Here, using electrostatic theory, we have studied the role of the dipolar terminal charges in aggregation of the S3b–S4 helix pair of KvAP in the absence of any external field (V = 0). A system attains stability, when its potential energy reaches minimum values. We have shown that the presence of terminal dipole charges (1) change the total potential energy of the charges on S3b–S4, affecting the stabilization of the α-helix pair within the bilayer lipid membrane and (2) the C- and the N-termini of the α-helices favor a different dielectric medium for enhanced stability. Thus, the dipolar terminal charges play a significant role in the aggregation of the two neighboring α-helices.     

Influence of protein flexibility on the electrostatic energy landscape in gramicidin A

We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel.     

Effective pore radius of the gramicidin channel. Electrostatic energies of ions calculated by a three-dielectric model.

Electrostatic calculation of the gramicidin channel is performed on the basis of a three-dielectric model in which the peptide backbone of the channel is added as a third dielectric region to the conventional two-dielectric channel model (whose pore radius is often referred to as the effective pore radius reff). A basic principle for calculating electrostatic fields in three-dielectric models is introduced. It is shown that the gramicidin channel has no unique value of reff. The reff with respect to the "self-image energy" (i.e., the image energy in the presence of a single ion) is 2.6-2.7 A, slightly depending upon the position of the ion (the least-square value over the whole length of the pore is 2.6 A). In contrast, the reff with respect to the electric potential due to an ion (and hence the reff with respect to the interaction energy between two ions) is dependent upon the distance s of separation; it ranges from 2.6 to greater than 5 A, increasing with an increase in s. However, for the purpose of rough estimation, the reff with respect to the self-image energy can also be used in calculating the electric potential and the interaction energy, because the error introduced by this approximation is an overestimation of the order of 30% at most. It is also shown that the apparent dielectric constant for the interaction between two charges depends markedly upon the positions of the charges. In the course of this study, the dielectric constant and polarizability of the peptide backbone in the beta-sheet structure is estimated to be 10 and 8.22 A3.     

Single channel and monolayer studies of acylated gramicidin A: influence of the length of the alkyl group

Three different gramicidin A analogues bearing acyl chains of various length on the ethanolamine moiety have been studied by investigating their single channel behaviour and their monolayer properties. It is shown that the single channel conductance does not depend on the substitution of the ethanolamine OH group and that the channel lifetime is roughly proportional to the length of the alkyl chain. The monolayer study indicates that acylation of gramicidin A produces compounds which have medium-dependent conformations. These acylated compounds are miscible with lipids, while GA is not, and the surface potential is not modified by the esterification of the alcohol group. Offprint requests to: F. Heitz     

Investigating the dielectric effects of channel pore water on the electrostatic barriers of the permeation ion by the finite difference Poisson-Boltzmann method

In this paper, the finite difference Poisson-Boltzmann (FDPB) method with four dielectric constants is developed to study the effect of dielectric saturation on the electrostatic barriers of the permeation ion. In this method, the inner shape of the channel pore is explicitly represented, and the fact that the dielectric constant inside the channel pore is different from that of bulk water is taken into account. A model channel system which is a right-handed twist bundle with four α-helical segments is provided for this study. From the FDPB calculations, it is found that the difference of the ionic electrostatic solvation energy for wider domains depends strongly on the pore radius in the vicinity of the ion when the pore dielectric constant is changed from 78 to 5. However, the electrostatic solvation energy of the permeation ion can not be significantly affected by the dielectric constant in regions with small pore radii. Our results indicate that the local electrostatic interactions inside the ion channel are of major importance for ion electrostatic solvation energies, and the effect of dielectric saturation on the electrostatic barriers is coupled to the interior channel dimensions. Received: 28 January 1997 / Accepted: 24 September 1997     

Modulating dipoles for structure-function correlations in the gramicidin A channel.

Dipoles of the tryptophan indole side chains have a direct impact on ion conductance in the gramicidin channel. Here, fluorination of the indoles (both 5- and 6-fluoro) is used to manipulate both the orientations and the magnitudes of the dipoles. The orientations and positions with respect to the channel axis were determined using (2)H solid state NMR of uniformly aligned lipid bilayer preparations. By exchange of the remaining four protons in the indole ring for deuterium, comparison could be made to d(5)-indole spectra that have previously been recorded for each of the four indoles of gramicidin A. After making the assignments which were aided by the observation of (19)F-(2)H dipolar interactions, we found that fluorination caused only minor changes in side chain conformation. With the high-resolution structural characterization of the fluorinated indoles in position 11, 13, and 15, the electrostatic interactions with a cation at the channel and bilayer center can be predicted and the influence of the modified dipoles on ion conductance estimated. The importance of the long-range electrostatic interaction was recently documented with the observation of alpha-helical dipoles oriented toward the bilayer center on the ion conductance pathway for the Streptomyces K(+) channel. We present direct measurements of the orientation of gramicidin channel F-Trp positions for use in analysis of dipole effects on channel permeation.     

Ionic permeation free energy in gramicidin: a semimicroscopic perspective

Ion permeation through the gramicidin channel is studied using a model that circumvents two major difficulties inherent to standard simulational methods. It exploits the timescale separation between electronic and structural contributions to dielectric stabilization, accounting for the influence of electronic polarization by embedding the channel in a dielectric milieu that describes this polarization in a mean sense. The explicit mobile moieties are the ion, multipolar waters, and the carbonyls and amides of the peptide backbone. The model treats the influence of aromatic residues and the membrane dipole potential. A new electrical geometry is introduced that treats long-range electrostatics exactly and avoids problems related to periodic boundary conditions. It permits the translocating ion to make a seamless transition from nearby electrolyte to the channel interior. Other degrees of freedom (more distant bulk electrolyte and nonpolar lipid) are treated as dielectric continua. Reasonable permeation free energy profiles are obtained for potassium, rubidium, and cesium; binding wells are shallow and the central barrier is small. Estimated cationic single-channel conductances are smaller than experiment, but only by factors between 2 (rubidium) and 50 (potassium). When applied to chloride the internal barrier is large, with a corresponding miniscule single-channel conductance. The estimated relative single-channel conductances of gramicidin A, B, and C agree well with experiment.     

Synthesis, characterization, and black lipid membrane studies of [7-L-alanine] gramicidin A

With a view to study the relevance of side-chain orientation in the transport of cations through a gramicidin transmembrane channel and to identify an analogue with favorable characteristics, [L-Ala7] gramicidin A was synthesized, purified, verified, and characterized by high-performance liquid chromatography, by carbon-13 and proton magnetic resonance spectra, and by circular dichroism spectra in methanol. Complete incorporation as the channel state was achieved when packaged in lysolecithin-containing lipid bilayers. The single-channel conductance data in diphytanoyllecithin/n-decane membranes are presented along with those of synthetic gramicidin A (GA). [L-Ala7] GA exhibits the highest most probable single-channel conductance so far reported for an analogue occurring at 28 pS as compared to 21 pS for GA under similar conditions. Also, a dramatic reduction in the dispersity of conducting states is observed with about 76% of the events falling in a narrow 1.75-pS conductance window as compared to about 31% of the events for GA under identical conditions. Thus, with the above characteristics, [L-Ala7]GA appears to be a very good candidate for a thorough study of ionic mechanism. The present results indicate that elements intrinsic to the channel proper are rate-limiting for GA and that there is no interfacial polarization or diffusion-controlled association at 1 M KCl and a 100-mV applied potential.     

Interaction of K+ ion with the solvated gramicidin A transmembrane channel.

Using Urry's gramicidin A (GA) atomic coordinates and ab into calculations, the interaction energies of a K+ ion with GA are examined. From these energies the values of the fitting parameters are obtained for 6-12-1 atom-atom pair potentials. The potential of the GA channel as experienced by the ion is analyzed in detail. An energy profile of the K+ ion in the GA channel is obtained by analyzing iso-energy maps. Using Monte Carlo simulations, the energy profiles of the K+ ion with the solvated GA channel are analyzed and the hydration structures in the presence of the K+ ion are studied.     

Temperature-jump and voltage-jump experiments at planar lipid membranes support an aggregational (micellar) model of the gramicidin A ion channel

Summary The kinetics of formation and dissociation of channels formed by gramicidin A and two analogues in planar lipid membranes was studied using a laser temperature-jump technique developed earlier [Brock, W., Stark, G., Jordan, P.C. (1981),Biophys. Chem. 13:329–348]. The time course of the electric current was found to agree with a single exponential term plus a linear drift. In case of gramicidin A the relaxation time was identical to that reported for V-jump experiments [Bamberg, E., Läuger, P. (1973),J. Membrane Biol. 11:177–194], which were interpreted on the basis of a dimerization reaction. The same results were obtained for gramicidin A and for chemically dimerized malonyl-bis-desformylgramicidin. It is therefore suggested that the dimerization represents a parallel association of two dimers to a tetramer. There is evidence that the tetramer, contrary to the presently favored dimer hypothesis, is the smallest conductance unit of an active gramicidin channel. An additional V-jump-induced relaxation process of considerably larger time constant is interpreted as a further aggregation of gramicidin dimers.Abbreviations GA gramicidin A - OPG O-pyromellitylgramicidin A - MBDG malonyl-bis-desformylgramicidin     

Local Anesthetics Affect Gramicidin A Channels via Membrane Electrostatic Potentials

The effects of local anesthetics (LAs), including aminoamides and aminoesters, on the characteristics of single gramicidin A (GA) channels in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers were studied. Aminoamides, namely lidocaine (LDC), prilocaine (PLC), mepivacaine (MPV), and bupivacaine (BPV), reduced the conductance of GA channels. Aminoesters influenced the current fluctuations induced by GA differently; procaine (PC) did not affect the fluctuations, whereas tetracaine (TTC) distinctly reduced the conductance of single GA channels. Using electrophysiological technique, we estimated the changes in the membrane boundary potential at the adsorption of LAs; LDC, PLC, MPV, BPV, and TTC substantially increased, while PC did not affect it. To elucidate which component of the membrane boundary potential, the surface or dipole potential, is responsible for the observed effects of LAs, we employed a fluorescence assay. We found that TTC led to a significant increase in the membrane dipole potential, whereas the adsorption of LDC, PLC, MPV, BPV, and PC did not produce any changes in the membrane dipole potential. We concluded that aminoamides affected the surface potential of lipid bilayers. Together, these data suggest that the effects of LAs on the conductance of single GA channels are caused by their influence on membrane electrostatic potentials; the regulation of GA pores by aminoamides is associated with the surface potential of membranes, whereas TTC modulation of channel properties is predominantly due to changes in dipole potential of lipid bilayers. These data might provide some significant implications for voltage-gated ion channels of cell membranes.     

Electrostatic calculations for an ion channel. II. Kinetic behavior of the gramicidin A channel.

A theoretical model of the gramicidin A channel is presented and the kinetic behavior of the model is derived and compared with previous experimental results. The major assumption of the model is that the only interaction between ions in a multiply-occupied channel is electrostatic. The electrostatic calculations indicate in a multiply-occupied channel is electrostatic. The electrostatic calculations indicate that there will be potential wells at each end of the channel and, at high concentrations, that both wells can be occupied. The kinetics are based on two reaction steps: movement of the ion from the bulk solution to the well and movement between the two wells. The kinetics for this reaction rate approach are identical to those based on the Nernst-Planck equation in the limit where the movement between the two wells is rate limiting. The experimental results for sodium and potassium are consistent with a maximum of two ions per channel. To explain the thallium results it is necessary to allow three ions per channel. It is shown that this case is compatible with the electrostatic calculations if the presence of an anion is included. The theoretical kinetics are in reasonable quantitative agreement with the following experimental measurements: single channel conductance of sodium, potassium, and thallium; bi-ionic potential and permeability ratio between sodium-potassium and potassium-thallium; the limiting conductance of potassium and thallium at high applied voltages; current-voltage curves for sodium and potassium at low (but not high) concentrations; and the inhibition of sodium conductance by thallium. The results suggest that the potential well is located close to the channel mouth and that the conductance is partially limited by the rate going from the bulk solution to the well. For thallium, this entrance rate is probably diffusion limited.     

BioMOCA—a Boltzmann transport Monte Carlo model for ion channel simulation

With the recent availability of high-resolution structural information for several key ion channel proteins and large-scale computational resources, Molecular Dynamics has become an increasingly popular tool for ion channel simulation. However, the CPU requirements for simulating ion transport on time scales relevant to conduction still exceed the resources presently available. To address this problem, we have developed Biology Monte Carlo (BioMOCA), a three-dimensional (3D) coarse-grained particle ion channel simulator based on the Boltzmann Transport Monte Carlo (BTMC) methodology. Although this approach is widely employed in the engineering community to study charge transport in electron devices, its application to molecular biology and electrolytes in general is new and hence must be validated. The pair correlation function, which is a measure of the microscopic structure of matter, provides a suitable benchmark to compare the BTMC method against the well-established Equilibrium Monte Carlo (EMC) approach. For validation purposes BioMOCA is used to simulate several simple homogeneous equilibrium electrolytes at concentrations of physiological interest. The ion–ion pair correlation functions computed from these simulations compare very well with those obtained from EMC simulations. We also demonstrate several performance-improving techniques that result in a several-fold speed-up without compromising the pair correlation function. BioMOCA is then used to perform full 3D simulations of ion transport in the gramicidin A channel in situ in a membrane environment, as well as to study the link between the electrostatic and dielectric properties of the protein and the channel's selectivity.     

Extended dipolar chain model for ion channels: electrostriction effects and the translocational energy barrier.

We reinvestigate the dipolar chain model for an ion channel. Our goal is to account for the influence that ion-induced electrostriction of channel water has on the translocational energy barriers experienced by different ions in the channel. For this purpose, we refine our former model by relaxing the positional constraint on the ion and the water dipoles and by including Lennard-Jones contributions in addition to the electrostatic interactions. The positions of the ion and the waters are established by minimization of the free energy. As before, interaction with the external medium is described via the image forces. Application to alkali cations show that the short range interactions modulate the free energy profiles leading to a selectivity sequence for translocation. We study the influence of some structural parameters on this sequence and compare our theoretical predictions with observed results for gramicidin.     

Transverse relaxation optimized 3D and 4D 15N/15N separated NOESY experiments of 15N labeled proteins

Distance constraints are an important complement to orientational constraints. While a high-resolution monomer structure of the ion channel forming polypeptide, gramicidin A, has been solved with 120 orientational constraints, the precise geometry of the dimer interface has not been characterized. Here, using both ¹³C and ¹⁵N labeled gramicidin A samples in hydrated phospholipid bilayers, both inter- and intramolecular distances have been measured with a recently developed simultaneous frequency and amplitude modulation (SFAM) solid-state NMR scheme. Using this approach ¹⁵N-¹³C₁ residual dipolar couplings across a hydrogen bond as small as 20 ± 2 Hz have been characterized. While such distances are on the order of 4.2 ± 0.2 Å, the spectroscopy is complicated by rapid global motion of the molecular structure about the bilayer normal and channel axis. Consequently, the nominal 40 Hz dipolar coupling is averaged depending on the orientation of the internuclear vector with respect to the motional axis. The intermolecular distance confirmed the previously described monomeric structure, while the intramolecular distance across the monomer–monomer interface defined this junction and confirmed the previous model of this interface.     

Formamidinium-induced dimer stabilization and flicker block behavior in homo- and heterodimer channels formed by gramicidin A and N-acetyl gramicidin A.

Compared to the N-formyl gramicidin A (GA), the N-acetyl gramicidin A (NAG) channel has unchanged conductance in 1 M NH4+ (gamma NN/gamma GG = 1, conductance ratio) but reduced conductance in 1 M K+ (gamma NN/gamma GG = 0.6) methylammonium (gamma NN/gamma GG = 0.3), and formamidinium (gamma NN/gamma GG = 0.1) solutions. Except with formamidinium, "flicker blocks" are evident even at low cutoff frequencies. For all cations studied, channel lifetimes of N-acetyl homodimers (NN) are approximately 50-fold shorter than those of the GA homodimer (GG). The novel properties of GA channels in formamidinium solution (supralinear current-voltage relations and dimer stabilization (Seoh and Busath, 1993)) also appear in NN channels. The average single channel lifetime in 1 M formamidinium solution at 100 mV is 6-7-fold longer than in K+ and methylammonium solutions and, like in the GA channel, significantly decreases with increasing membrane potential. Experiments with mixtures of the two peptides, GA and NAG, showed three main conductance peaks. Oriented hybrids were formed utilizing the principle that monomers remain in one leaflet of the bilayer (O'Connell et al., 1990). With GA at the polarized side and NAG at the grounded side, at positive potentials (in which case hybrids were designated GN) and at negative potentials (in which case hybrids were designated NG), channels had the same conductances and channel properties at all potentials studied. Flicker blocks were not evident in the hybrid channels, which suggests that both N-acetyl methyl groups at the junction of the dimer are required to cause flickers. Channel lifetimes in hybrids are only approximately threefold shorter than those of the GG channels, and channel conductances are similar to those of GG rather than NN channels. We suggest that acetyl-acetyl crowding at the dimeric junction in NN channels cause dimer destabilization, flickers, and increased selectivity in N-acetyl gramicidin channels.     

Energy levels and ion wave functions in gramicidin channels

A model study of the motion of Na+ ions in the cavity of membrane gramicidin channels was performed by the methods of quantum mechanics. An approximation of the distribution of the electrostatic potential along the channel axis, determined by charges on the atoms of the gramicidin A molecule, was obtained. The energy distribution and the wave functions for the stationary states of the ions were determined. The solutions of the Schr?dinger equation for two conformers were compared.     

The Effect of the Amino-Acid Side Chains on the Energy Profiles for Ion Transport in the Gramicidin A Channel

Abstract

Computations on the energy profiles for Na⁺ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed in its most stable conformation, 2) with the tail allowed to optimize its conformation upon the progression of the ion. In both approximations the overall shape of the energy profile is very similar to that obtained in the absence of the side chains. One observes, however, a general lowering of the profile upon the adjunction of the side chains. The analysis of the factors responsible for this energy lowering indicates that it is due essentially to the electrostatic and polarisation components of the interaction which interplay differently, however, in the different parts of the channel. A particular role is attributed in this respect to the tryptophan residues of GA. The role of the 4 tryptophans present, Trp 15, 13, 11 and 9, is individualized by stripping of one of them at a time. The strongest effect on the energy deepening is due to Trp 13 and is particularly prominent in the entrance zone at 14.5Å from the center of the channel. The result indicates the possibility of investigating theoretically the effect on the energy profiles of the substitution of the “natural” side chain by others.     

Membrane surface-charge titration probed by gramicidin A channel conductance.

We manipulate lipid bilayer surface charge and gauge its influence on gramicidin A channel conductance by two strategies: titration of the lipid charge through bulk solution pH and dilution of a charged lipid by neutral. Using diphytanoyl phosphatidylserine (PS) bilayers with CsCl aqueous solutions, we show that the effects of lipid charge titration on channel conductance are masked 1) by conductance saturation with Cs+ ions in the neutral pH range and 2) by increased proton concentration when the bathing solution pH is less than 3. A smeared charge model permits us to separate different contributions to the channel conductance and to introduce a new method for "bilayer pKa" determination. We use the Gouy-Chapman expression for the charged surface potential to obtain equilibria of protons and cations with lipid charges. To calculate cation concentration at the channel mouth, we compare different models for the ion distribution, exact and linearized forms of the planar Poisson-Boltzmann equation, as well as the construction of a "Gibbs dividing surface" between salt bath and charged membrane. All approximations yield the intrinsic pKain of PS lipid in 0.1 M CsCl to be in the range 2.5-3.0. By diluting PS surface charge at a fixed pH with admixed neutral diphytanoyl phosphatidylcholine (PC), we obtain a conductance decrease in magnitude greater than expected from the electrostatic model. This observation is in accord with the different conductance saturation values for PS and PC lipids reported earlier (, Biochim. Biophys. Acta. 552:369-378) and verified in the present work for solvent-free membranes. In addition to electrostatic effects of surface charge, gramicidin A channel conductance is also influenced by lipid-dependent structural factors.