Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects

The nature of proton transduction (PTR) through a file of water molecules, along the gramicidin A (gA) channel, has long been considered as being highly relevant to PTR in biological systems. Previous attempts to model this process implied that the so-called Grotthuss mechanism and the corresponding orientation of the water file plays a major role. The present work reexamines the PTR in gA by combining a fully microscopic empirical valence bond (EVB) model and a recently developed simplified EVB-based model with Langevin dynamics (LD) simulations. The full model is used first to evaluate the free energy profile for a stepwise PTR process. The corresponding results are then used to construct the effective potential of the simplified EVB. This later model is then used in Langevin dynamics simulations, taking into account the correct physics of possible concerted motions and the effect of the solvent reorganization. The simulations reproduce the observed experimental trend and lead to a picture that is quite different from that assumed previously. It is found that the PTR in gA is controlled by the change in solvation energy of the transferred proton along the channel axis. Although the time dependent electrostatic fluctuations of the channel and water dipoles play their usual role in modulating the proton-transfer process (Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 444), the PTR rate is mainly determined by the free energy profile. Furthermore, the energetics of the reorientation of the unprotonated water file do not appear to provide a consistent way of assessing the activation barrier for the PTR process. It seems to us that in the case of gA, and probably other systems with significant electrostatic barriers for the transfer of the proton charge, the PTR rate is controlled by the electrostatic barrier. This finding has clear consequences with regards to PTR processes in biological systems.     

Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method

The large interest in long-range proton transfer in biomolecules is triggered by its importance for many biochemical processes such as biological energy transduction and drug detoxification. Since long-range proton transfer occurs on a microsecond time scale, simulating this process on a molecular level is still a challenging task and not possible with standard simulation methods. In general, the dynamics of a reactive system can be described by a master equation. A natural way to describe long-range charge transfer in biomolecules is to decompose the process into elementary steps which are transitions between microstates. Each microstate has a defined protonation pattern. Although such a master equation can in principle be solved analytically, it is often too demanding to solve this equation because of the large number of microstates. In this paper, we describe a new method which solves the master equation by a sequential dynamical Monte Carlo algorithm. Starting from one microstate, the evolution of the system is simulated as a stochastic process. The energetic parameters required for these simulations are determined by continuum electrostatic calculations. We apply this method to simulate the proton transfer through gramicidin A, a transmembrane proton channel, in dependence on the applied membrane potential and the pH value of the solution. As elementary steps in our reaction, we consider proton uptake and release, proton transfer along a hydrogen bond, and rotations of water molecules that constitute a proton wire through the channel. A simulation of 8 mus length took about 5 min on an Intel Pentium 4 CPU with 3.2 GHz. We obtained good agreement with experimental data for the proton flux through gramicidin A over a wide range of pH values and membrane potentials. We find that proton desolvation as well as water rotations are equally important for the proton transfer through gramicidin A at physiological membrane potentials. Our method allows to simulate long-range charge transfer in biological systems at time scales, which are not accessible by other methods.     

Wavelength-selective fluorescence in ion channels formed by gramicidin A in membranes

Gramicidins are linear peptides that form ion channels that are specific for monovalent cations in membranes. The tryptophan residues in the gramicidin channel play a crucial role in the organization and function of the channel. The natural mixture of gramicidins, denoted as gramicidin A’, consists of mostly gramicidin A, but also contains gramicidins B, C and D as minor components. We have previously shown that the tryptophan residues in ion channels formed by the naturally occurring peptide, gramicidin A’, display wavelength-dependent fluorescence characteristics due to the motionally restricted environment in which they are localized. In order to check the influence of ground-state heterogeneity in the observed wavelength-selective fluorescence of gramicidin A’ in membranes, we performed similar experiments with pure gramicidin A in model membranes. Our results show that the observed wavelength-selective fluorescence characteristics of naturally occurring gramicidin A’ are not due to ground-state heterogeneity.     

Ion solvation by channel carbonyls characterized by 17O solid-state NMR at 21 T

Recently available ultrahigh magnetic fields offer new opportunities for studies of quadrupole nuclei in biological solids because of the dramatic enhancement in sensitivity and resolution associated with the reduction of second-order quadrupole interactions. Here, we present a new approach for understanding the function and energetics of ion solvation in channels using solid-state 17O NMR spectroscopy of single-site 17O-labeled gramicidin A. The chemical shift and quadrupole coupling parameters obtained in powder samples of lyophilized material are similar to those shown in the literature for carbonyl oxygens. In lipid bilayers, it is found that the carbonyl 17O anisotropic chemical shift of Leu10, one of the three carbonyl oxygens contributing to the ion binding site in gramicidin A, is altered by 40 ppm when K+ ion binds to the channel, demonstrating a high sensitivity to such interactions. Moreover, considering the large breadth of the carbonyl 17O chemical shift (>500 ppm), the recording of anisotropic 17O chemical shifts in bilayers aligned with respect to magnetic field B0 offers high-quality structural restraints similar to 15N and 13C anisotropic chemical shifts.     

Effect of membrane environment on proton permeation through gramicidin A channels

Multistate empirical valence bond simulations were employed to study proton transport through gramicidin A channels embedded in two different lipid bilayers, glycerol 1-monooleate (GMO) and diphytanolphosphatidylcholine (DiPhPC). Free energy barriers to proton permeation were derived using a new internal reaction coordinate describing the proton permeation process. The large quantitative and qualitative differences between the two systems are discussed in terms of local bilayer structures, ordering of interfacial water, and channel flexibility in the two environments.     

A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadine

The mechanism of inhibition of the influenza A virus M2 proton channel by the antiviral drug amantadine has been under intense investigation. The importance of a mechanistic understanding is heightened by the prevalence of amantadine-resistant mutations. To gain mechanistic insight at the molecular level, we carried out extensive molecular dynamics simulations of the tetrameric M2 proton channel in both apo and amantadine-bound forms in a lipid bilayer. The simulation of the apo form revealed that Val27 from the four M2 subunits can form a secondary gate near the channel entrance and break the water wire in the channel pore. This gate arises from physical occlusion and the elimination of hydrogen-bonding partners for water molecules. In the presence of amantadine, the secondary gate formed by Val27 and the drug molecule lying just below form an extended blockage, which breaks the water wire throughout the simulation. The location and orientation of amantadine inside of the channel pore as found in our simulation are supported by a host of experimental observations. Our study suggests a novel role for Val27 in the inhibition of the M2 proton channel by amantadine.     

Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl

Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.     

Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.     

Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

Phospholipid chain length alters the equilibrium between pore and channel forms of gramicidin

Gramicidin is an excellent model system for studying the passage of ions through biological membranes. The conformation of gramicidin is well defined in many different solvent and lipid systems, as are its conductance and spectroscopic properties. It is a polymorphic molecule that can adopt two different types of structure, the double helical "pore" and the helical dimer "channel". This study investigated the influence of the acyl chain length of membrane phospholipids on the conformations adopted by gramicidin. We used circular dichroism spectroscopy to examine the conformational equilibrium between the pore and channel forms in small unilamellar vesicles of phosphatidylcholine with acyl chain lengths of 18, 20 and 22 carbons. Our results show that in C18 and C20 lipids almost all the gramicidin is in the channel form, while in the longer C22 lipids the equilibrium shifts in favour of pore conformations, such that they form up to 43% of the total population. This change is attributed to the ability of the double helical conformation to tolerate more hydrophobic mismatch than the helical dimer, perhaps due to the greater number of stabilising intermolecular hydrogen bonds.     

Detection of single ion channel activity on a chip using tethered bilayer membranes

Membrane-bound ion channels are promising biological receptors since they allow for the stochastic detection of analytes at high sensitivity. For stochastic sensing, it is necessary to measure the ion currents associated with single ion channel opening and closing events. However, this calls for stability, high reproducibility, and long lifetimes. A critical issue to overcome is the low stability of the ion channel environment, that is, the bilayer membrane. A promising technique to surmount this is to connect the lower part of the membrane to a surface forming a tethered bilayer membrane. By reconstituting the synthetic ion channel, gramicidin A, into a tethered bilayer as part of a microchip design, we have been able to record the activity of single ion channels. The observed activity was compared with that obtained by a conventional electrophysiology method, tip dipping, to confirm its authenticity. These findings allow for the construction of stable biosensors based on ion channels and provide a novel technique for the characterization of ion channel activity.     

Inhibition of Ion Transport through Gramicidin A Channels by the Addition of Local Anesthetic Procaine

The blocking effects of the cationic procaine, a typical local anesthetic (LA), on ion transport through gramicidin A (gA) channels between two aqueous phases (W1 and W2) were electrochemically elucidated. Although the gA channels promoted the permeation of monovalent cations, especially Cs⁺, the addition of procaine to W1 decreased the permeation of Cs⁺ through these channels from W1 to W2. This can be explained based on the following mechanism. Hydrophobic cationic procaine tends to approach the pore of a gA channel. Since it is too large to enter the pore, it cannot pass through the channel. Thus, cationic procaine inhibits the permeation of Cs⁺ from W1 to W2 by competing with Cs⁺ for access to the entrances of the gA channels. It is postulated that the decrease in the apparent activity of Cs⁺ caused by this competition prevents ion transport through the gA channels.     

Implementation of a molecular dynamics approach with rigid fragments to simulation of chemical reactions in biomolecular systems

We describe a new implementation of the molecular dynamics method aimed at simulation of the properties of biomolecular systems in which chemical reactions are possible. The quantum mechanical/molecular mechanical method based on the effective fragment potential theory is used for calculating the energies and forces along trajectories. Due to specific features of the effective fragment theory, the behavior of the molecular mechanical subsystem is described by rigid body dynamics. The method has been applied to simulation of proton transfer along the chain of water molecules inside the gramicidin channel.     

Sulfonated 2D Covalent Organic Frameworks for Efficient Proton Conduction

Open 1D channels found in covalent organic frameworks are unique and promising to serve as pathways for proton conduction; how to develop high-rate yet stable transporting systems remains a substantial challenge. Herein, this work reports a strategy for exploring proton-conducting frameworks by engineering pore walls and installing proton-containing polymers into the pores. Amide-linked and sulfonated frameworks were synthesized from imine-linked precursors via sequentially engineering to oxidize into amide linkages and to further anchor sulfonic acid groups onto the pore walls, enabling the creation of sulfonated frameworks with high crystallinity and channel ordering. Integrating sulfonated polyether ether ketone chains into the open channels enables proton hopping to across the channels, greatly increases proton conductivity and enables a stable continuous run. These results suggest a way to explore proton-conducting COFs via systematic engineering of the wall and space of the open nanochannels.     

Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel

The structure and function of the influenza A M2 proton channel have been the subject of intensive investigations in recent years because of their critical role in the life cycle of the influenza virus. Using a truncated version of the M2 proton channel (i.e., M2TM) as a model, here we show that fluctuations in the fluorescence intensity of a dye reporter that arise from both fluorescence quenching via the mechanism of photoinduced electron transfer (PET) by an adjacent tryptophan (Trp) residue and local motions of the dye molecule can be used to probe the conformational dynamics of membrane proteins. Specifically, we find that the dynamics of the conformational transition between the N-terminal open and C-terminal open states of the M2TM channel occur on a timescale of about 500 μs and that the binding of either amantadine or rimantadine does not inhibit the pH-induced structural equilibrium of the channel. These results are consistent with the direct occluding mechanism of inhibition which suggests that the antiviral drugs act by sterically occluding the channel pore.     

Gating Mechanism of the Voltage-Gated Proton Channel Studied by Molecular Dynamics Simulations

The voltage-gated proton channel Hv1 has important roles in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The Hv1 channel has also been found to be highly expressed in cell lines and tissue samples from patients with breast cancer. A high-resolution closed-state structure has been reported for the mouse Hv1 chimera channel (mHv1cc), solved by X-ray crystallography, but the open-state structure of Hv1 has not been solved. Since Hv1 is a promising drug target, various groups have proposed open conformations by molecular modeling and simulation studies. However, the gating mechanism and the open-state conformation under the membrane potential are still debate. Here, we present a molecular dynamics study considering membrane potential and pH conditions. The closed-state structure of mHv1cc was used to run molecular dynamics (MD) simulations with respect to electric field and pH conditions in order to investigate the mechanism of proton transfer. We observed a continuous hydrogen bond chain of water molecules called a water-wire to be formed through the channel pore in the channel opening, triggered by downward displacement of the S2 helix and upward movement of the S4 helix relative to other helices. Due to the movement of the S2 and S4 helices, the internal salt bridge network was rearranged, and the hydrophobic gating layers were destroyed. In line with previous experimental and simulation observations, our simulation results led us to propose a new gating mechanism for the Hv1 proton channel, and may provide valuable information for novel drug discovery.     

Simulation of proton transport in the gramicidin A channel

The free energy profiles for proton transfer along the oriented water file inside the gramicidin A channel were calculated. An original implementation of the rigid-body molecular dynamics method was used for describing the peptide groups of the channel and outer water molecules. The inner water wire was simulated using the PM6 force field parameters, which adequately describe the formation and cleavage of chemical and hydrogen bonds in water molecules. Different mechanisms of proton transfer through the gramicidin A channel were considered, namely, proton H⁺ translocation, transfer of the anion defect OH^?, and reorientation of the water file inside the channel. To facilitate parallel calculations of trajectories, the reaction coordinate was divided into segments, and the results were combined by the weighted histogram analysis method. The first two processes, H⁺ and OH^? transfers, were shown to be barrierless. Only the stage of reorientation of the water file inside the channel has an energy barrier.     

Role of solvation dynamics in excited state proton transfer of 1-naphthol in nanoscopic water clusters formed in a hydrophobic solvent

Excited state proton transfer (ESPT) in biologically relevant organic molecules in aqueous environments following photoexcitation is very crucial as the reorganization of polar solvents (solvation) in the locally excited (LE) state of the organic molecule plays an important role in the overall rate of the ESPT process. A clear evolution of the two photoinduced dynamics in a model ESPT probe 1-naphthol (NpOH) upon ultrafast photoexcitation is the motive of the present study. Herein, the detailed kinetics of the ESPT reaction of NpOH in water clusters formed in hydrophobic solvent are investigated. Distinct values of time constants associated with proton transfer and solvent relaxation have been achieved through picosecond-resolved fluorescence measurements. We have also used a model solvation probe Coumarin 500 (C500) to investigate the dynamics of solvation in the same environmental condition. The temperature dependent picosecond-resolved measurement of ESPT of NpOH and the dynamics of solvation from C500 identify the magnitude of intermolecular hydrogen bonding energy in the water cluster associated with the ultrafast ESPT process.     

Solution reaction space Hamiltonian based on an electrostatic potential representation of solvent dynamics

Quantum chemical solvation models usually rely on the equilibrium solvation condition and is thus not immediately applicable to the study of nonequilibrium solvation dynamics, particularly those associated with chemical reactions. Here we address this problem by considering an effective Hamiltonian for solution-phase reactions based on an electrostatic potential (ESP) representation of solvent dynamics. In this approach a general ESP field of solvent is employed as collective solvent coordinate, and an effective Hamiltonian is constructed by treating both solute geometry and solvent ESP as dynamical variables. A harmonic bath is then attached onto the ESP variables in order to account for the stochastic nature of solvent dynamics. As an illustration we apply the above method to the proton transfer of a substituted phenol-amine complex in a polar solvent. The effective Hamiltonian is constructed by means of the reference interaction site model self-consistent field method (i.e., a type of quantum chemical solvation model), and a mixed quantum/classical simulation is performed in the space of solute geometry and solvent ESP. The results suggest that important dynamical features of proton transfer in solution can be captured by the present approach, including spontaneous fluctuations of solvent ESP that drives the proton from reactant to product potential wells.     

Excited State Photophysics of Curcumin and its Modulation in Alkaline Non-Aqueous Medium

Curcumin, a well-known medicinal pigment, has seen limited applications in biology despite having great potential as a therapeutic drug. Deprotonation is one of the possible ways to enhance solubility of curcumin in polar solvent. Here, we have explored the effect of deprotonation on the ultrafast dynamics of this biomolecule with the help of the time-resolved fluorescence spectroscopic measurements using the femtosecond fluorescence upconversion technique. The excited state photophysics of fully deprotonated curcumin significantly differs from that of neutral curcumin. We have observed that the completely deprotonated curcumin not only has higher quantum yield, but also higher excited state lifetime and slower solvation dynamics in comparison to neutral curcumin. We propose solvation dynamics and intramolecular charge transfer as the excited state processes associated with the radiative decay of the completely deprotonated molecule, while ruling out the possibility of excited state proton exchange or proton transfer. Our results are well supported by time-dependent density-functional theory calculations. Lastly, we have also demonstrated the possibility of modulating the ultrafast dynamics of fully deprotonated curcumin using non-aqueous alkaline binary solvent mixtures. We believe our results will provide significant physical insight towards unveiling the excited state dynamics of this molecule.