Semisynthesis and folding of the potassium channel KcsA

In this contribution we describe the semisynthesis of the potassium channel, KcsA. A truncated form of KcsA, comprising the first 125 amino acids of the 160-amino acid protein, was synthesized using expressed protein ligation. This truncated form corresponds to the entire membrane-spanning region of the protein and is similar to the construct previously used in crystallographic studies on the KcsA protein. The ligation reaction was carried out using an N-terminal recombinant peptide alpha-thioester, corresponding to residues 1-73 of KcsA, and a synthetic C-terminal peptide corresponding to residues 74-125. Chemical synthesis of the C-peptide was accomplished by optimized Boc-SPPS techniques. A dual fusion strategy, involving glutathione-S-transferase (GST) and the GyrA intein, was developed for recombinant expression of the N-peptide alpha-thioester. The fusion protein, expressed in the insoluble form as inclusion bodies, was refolded and then cleaved successively to remove the GST tag and the intein, thereby releasing the N-peptide alpha-thioester. Following chemical ligation, the KcsA polypeptide was folded into the tetrameric state by incorporation into lipid vesicles. The correctness of the folded state was verified by the ability of the KcsA tetramer to bind to agitoxin-2. To our knowledge, this work represents the first reported semisynthesis of a polytopic membrane protein and highlights the potential application of native chemical ligation and expressed protein ligation for the (semi)synthesis of integral membrane proteins.     

Cooperative transport in a potassium ion channel

Our current understanding of ion permeation through the selectivity filter of the KcsA potassium channel is based on the concept of a multi-ion transport mechanism. The details of this concerted movement, however, are not well understood. In the present paper we report on molecular dynamics simulations which provides new insights. It is shown that ion translocation is based on the collective hopping of ions and water molecules which is mediated by the flexible charged carbonyl groups lining the backbone of the pore. In particular, there is strong evidence for pairwise translocations where one ion and one water molecule form a bound state. We suggest a physical explanation of the observed phenomena employing a simple lattice model. It is argued that the water molecules can act as rectifiers during the hopping of ion-water pairs.     

Structure and ion selectivity of the open potential-dependent potassium channel

The structure and ion selectivity of the potential-dependent potassium channel is investigated. It is shown that the channel constructed by joining the α-subunit with the β-subunit concave, when the axial symmetry axes coincide, is the potential-dependent potassium channel in the open state.     

Oriented reconstitution of a membrane protein in a giant unilamellar vesicle: experimental verification with the potassium channel KcsA

We report a method for the successful reconstitution of the KcsA potassium channel with either an outside-out or inside-out orientation in giant unilamellar vesicles, using the droplet-transfer technique. The procedure is rather simple. First, we prepared water-in-oil droplets lined with a lipid monolayer. When solubilized KcsA was encapsulated in the droplet, it accumulated at monolayers of phosphatidylglycerol (PG) and phosphoethanolamine (PE) but not at a monolayer of phosphatidylcholine (PC). The droplet was then transferred through an oil/water interface having a preformed monolayer. The interface monolayer covered the droplet so as to generate a bilayer vesicle. By creating chemically different lipid monolayers at the droplet and oil/water interface, we obtained vesicles with asymmetric lipid compositions in the outer and inner leaflets. KcsA was spontaneously inserted into vesicles from the inside or outside, and this was accelerated in vesicles that contained PE or PG. Integrated insertion into the vesicle membrane and the KcsA orientation were examined by functional assay, exploiting the pH sensitivity of the opening of the KcsA when the pH-sensitive cytoplasmic domain (CPD) faces toward acidic media. KcsA loaded from the inside of the PG-containing vesicles becomes permeable only when the intravesicular pH is acidic, and the KcsA loaded from the outside becomes permeable when the extravesicular pH is acidic. Therefore, the internal or external insertion of KcsA leads to an outside-out or inside-out configuration so as to retain its hydrophilic CPD in the added aqueous side. The CPD-truncated KcsA exhibited a random orientation, supporting the idea that the CPD determines the orientation. Further application of the droplet-transfer method is promising for the reconstitution of other types of membrane proteins with a desired orientation into cell-sized vesicles with a targeted lipid composition of the outer and inner leaflets.     

Targeted molecular dynamics of an open-state KcsA channel

Pore opening of KcsA channel is studied using targeted molecular dynamics simulations. Conformational changes of the protein are determined, starting from the crystallized refined 2.0 A structure (pdb 1K4C) determined in x-ray experiments and arriving to the open-state structure constructed on the basis of electron paramagnetic resonance spectroscopic data (pdb 1JQ1). Our results corroborate the essential role played by the terminal residues located on the transmembrane helices M2 which were not taken into account at that time. The aperture mechanism of the channel appears to be ziplike. A small constraint (approximately equal to 5 x 10(-2) kcal mol(-1) A(-2) per C(alpha)) applied to the terminal residues located on the intracellular side is sufficient to initialize the pore opening at the innermost part of the gate, but additional constraint must be applied to definitely complete the pore aperture. The open structure is proved to be a metastable state since releasing the constraint leads to another relaxed open conformation which seems to reach stability.     

Insight into the origins of the barrier-less knock-on conduction in the KcsA channel: molecular dynamics simulations and ab initio calculations

Since the pioneering work of Zhou et al. (Y. Zhou, J. H. Morais-Cabral, A. Kaufman and R. MacKinnon, Nature, 2001, 414, 43-48) it is now well established that the streptomyces lividans potassium channel (KcsA) can accommodate more than one ion, namely between 2 and 3. As a result, it is usually assumed that the conduction of ions proceeds through a barrier-less knock-on mechanism. This one is an alternation of two sequences containing either 2 or 3 ions which have nearly the same energies. However, the origin of such knock-on mechanism is not clearly known. The entry and the exit of ion in or out of the selectivity filter are suspected to be due to the repulsive interactions between ions. In this work, molecular dynamics simulations running over nanoseconds have been done in order to identify such events. Two specific situations, namely (S(1), S(3)) containing 2 ions and (S(2), S(4)) containing 3 ions, have been investigated regarding the different locations that ions can occupy during their diffusion through the selectivity filter of KcsA. We show that contractions of the (S(1), S(3)) file and dilation of the (S(2), S(4)) file are at the origin of the passage from one sequence to the other. The comparison between the experimentally observed diffusion rate and the occurrence's frequency of such contractions or dilation confirm the importance of such events. Ab initio calculations have also been conducted in order to examine the effect of ion polarization in the filter of KcsA. During the contraction of the ion/water file, one charge at the extra-cellular mouth of the channel strongly deviates from the others. This behavior could guide the diffusion direction to a certain extent since the contraction of the (S(1), S(3)) is favored.     

Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity

The thermodynamic exclusion of Na+ relative to K+ in potassium channels is examined by calculating the distribution of binding energies for Na+ and K+ in a model of the selectivity filter of the KcsA potassium channel. These distributions are observed to take a surprisingly simple form: Gaussian with a slight positive skewness that is insignificant in the present context. Complications that might be anticipated from these distributions are not problematic here. Na+ occupies the filter with a mean binding energy substantially lower than that of K+. The difference is comparable to the difference in hydration free energies of Na+ and K+ in bulk aqueous solution. Thus, the average energies of binding to the filter do not discriminate Na+ from K+ when measured from a baseline of the difference in bulk hydration free energies. The strong binding of Na+ constricts the filter, consistent with a negative partial molar volume of Na+ in water in contrast with a positive partial molar volume of K+ in water. Discrimination in favor of K+)can be attributed to the scarcity of favorable binding configurations for Na+ compared to K+. That relative scarcity is quantified as enhanced binding energy fluctuations, which reflects both the energetically stronger binding of Na+ and the constriction of the filter induced by Na+ binding.     

Kinetic lattice grand canonical Monte Carlo simulation for ion current calculations in a model ion channel system

An algorithm in which kinetic lattice grand canonical Monte Carlo simulations are combined with mean field theory (KLGCMC/MF) is presented to calculate ion currents in a model ion channel system. In this simulation, the relevant region of the system is treated by KLGCMC simulations, while the rest of the system is described by modified Poisson-Boltzmann mean field theory. Calculation of reaction field due to induced charges on the channel/water and membrane/water boundaries is carried out using a basis-set expansion method [Im and Roux, J. Chem. Phys. 115, 4850 (2001)]. Calculation of ion currents, electrostatic potentials, and ion concentrations, as obtained from the KLGCMC/MF simulations, shows good agreement with Poisson-Nernst-Planck (PNP) theory predictions when the channel and membrane have the same dielectric constant as water. If the channel and membrane have a lower dielectric constant than water, however, there is a considerable difference between the KLGCMC/MF and PNP predictions. This difference is attributed to the reaction field, which is missing in PNP theory. It is demonstrated that the reaction field as well as fixed charges in the channel play key roles in selective ion transport. Limitations and further development of the current KLGCMC/MF approach are also discussed.     

Role of water molecules in the KcsA protein channel by molecular dynamics calculations

Molecular dynamics simulations supported by electrostatic calculations have been conducted on the KcsA channel to determine the role of water molecules in the pore. Starting from the X-ray structure of the KcsA channel in its closed state at 2.0 angstroms resolution, the opening of the pore towards a conformation built on the basis of EPR results is studied. We show that water molecules act as a structural element for the K+ ions inside the filter and the hydrophobic cavity of the channel. In the filter, water tends to enhance the depth of the wells occupied by the K+ ions, while in the cavity there is a strong correlation between the water molecules and the cavity ion. As a consequence, the protein remains very stable in the presence of three K+ ions in the selectivity filter and one in the cavity. The analysis of the dynamics of water molecules in the cavity reveals preferred orientations of the dipoles along the pore axis, and a correlated behavior between this dipole orientation and the displacement of the K+ ion during the gating process.     

Quantum mechanical calculations on selectivity in the KcsA channel: the role of the aqueous cavity

We have carried out quantum calculations on selected residues at the intracellular side of the selectivity filter of the KcsA potassium channel, using the published X-ray coordinates as starting points. The calculations involved primarily the side chains of residues lining the aqueous cavity on the intracellular side of the selectivity filter, in addition to water molecules, plus a K+ or Na+ ion. The results showed unambiguously that Na+ significantly distorts the symmetry of the channel at the entrance to the selectivity filter (at the residue T75), while K+ does so to a much smaller extent. In all, three ion positions have been calculated: the S4 (lowest) position at the bottom of the selectivity filter, the top of the cavity, and the midpoint of the cavity; Na+ is trapped at the cavity top, while K+ is cosolvated by the selectivity filter carbonyl groups plus threonine hydroxyl groups so that it can traverse the filter. Only one water molecule remains in the K+ solvation shell at the upper position in the cavity; this solvation shell also contains four threonine (T75) hydroxyl oxygens and two backbone carbonyls, while Na+ is solvated by five molecules of water and one oxygen from threonine hydroxyls. T75 at the entrance to the selectivity filter has a key role in recognition of the alkali ion, and T74 has secondary importance. The energetic basis for the preferential bonding of potassium by these residues is briefly discussed, based on additional calculations. Taken together, the results suggest that Na+ would have difficulty entering the cavity, and if it did, it would not be able to enter the selectivity filter.     

Lithium ion conduction in an organoborate zwitterion-LiTFSI mixture

An organoborate zwitterion-lithium salt mixture, prepared via selective borate formation of N-ethylimidazolium salt, exhibited ionic conductivity of 3.0 x 10(-5) S cm(-1) at 50 degrees C and a lithium transference number of 0.69.     

Kinetic modeling of industrial steam cracker

A comprehensive mathematical model is a very useful tool for the selection of feedstock, optimized cracker product mix, downstream production planning, and optimized plant performance. As a part of achieving this prime objective, a mathematical model has been developed for the simulation of the radiation section of a steam cracker unit. The model involves solving differential component, energy, and momentum balance equations numerically to generate temperature, concentration, and pressure profiles along the length of the reactor tube. The model has been developed in FORTRAN using the lSODE solver. The model considers 19 free radicals and 35 molecules connected over 433 reactions. The model was used to simulate the performance of propane and ethane cracking. The model predicted propane conversion is 95.55 against the plant data of 95% at a coil outlet temperature of 845 ​°C and the corresponding predicted ethylene and propylene yield is 34.49 and 11.53% respectively. The model has been validated for ethane cracking performance. The model predicted ethylene yield is in good agreement with that of plant values for ethane cracking. The model provides a basis for the optimization of process parameters for the given geometry. The model is useful to answer what-if questions and to investigate operational strategies.     

Kinetic modeling of pyrolysis of scrap tires

The disposal of used tires is a major environmental problem. With increasing interest on recovery of wastes, pyrolysis is considered as an alternative process for recovering some of the value in scrap tires. An accurate kinetic model is required to predict product yields during thermal or catalytic pyrolysis of scrap tires. Pyrolysis products contain a variety of hydrocarbons over a wide boiling range. A common approach for kinetic modeling of such complex systems is lumping where each lump is defined by a boiling point range. Available experimental data for thermal and catalytic pyrolysis of scrap tires from the literature were used to evaluate two types of lumping models; discrete and continuous lumping models. The lumps were described in terms of the boiling point distribution of the reactant mixture. In the discrete model, the conversion of heavier to lighter lumps was described in terms of series and parallel first order reactions. In the continuous model, the normalized boiling point was used to describe the reactant mixture as a continuous mixture. An optimization procedure was implemented for estimation of the model parameters using experimental data reported in the literature. Model predictions with indicated that although the discrete model could reasonably predict the yields of different cuts in the products, predictions of the continuous model were very good, especially in thermal pyrolysis.     

Electronic conduction in solid potassium permanganate excited by water molecules

Water molecules present as an interstitial impurity are found to induce electronic conduction in solid KMnO₄ with an activation energy of ? 0.28 eV. It is suggested that when ionic sites are surrounded by water molecules the high dielectric constant of the water lowers the activation energy associated with transfer of electrons between the donor-acceptor states involved in the hopping conduction.     

Understanding correlation effects for ion conduction in polymer electrolytes

Polymer electrolytes typically exhibit diminished ionic conductivity due to the presence of correlation effects between the cations and anions. Microscopically, transient ionic aggregates, e.g., ion-pairs, ion-triplets, or higher order ionic clusters, engender ionic correlations. Employing all-atom simulation of a model polymer electrolyte comprising of poly(ethylene oxide) and lithium iodide, the ionic correlations are explored through construction of elementary functions between pairs of the ionic species that qualitatively explains the spatio-temporal nature of these correlations. Furthermore, commencing from the exact Einstein-like equation describing the collective diffusivity of the ions in terms of the average diffusivity of the ions (i.e., the self-terms) and the correlations from distinct pairs of ions, several phenomenological parameters are introduced to keep track of the simplification procedure that finally boils down to the recently proposed phenomenological model by Stolwijk and Obeidi (SO) [Stolwijk, N. A.; Obeidi, S. Phys. Rev. Lett. 2004, 93, 125901]. The approximation parameters, which can be retrieved from simulations, point to the necessity of additional information in order to fully describe the correlation effects apart from the mere fraction of ion-pairs that apparently accounts for the correlations originating from only the nearest neighbor structural correlations. These parameters are close to, but are not exactly unity, as assumed in the SO model. Finally, as an application of the extended SO model, one is able to estimate the dynamics of the free and non-free ions as well as their fractions from the knowledge of the single particle diffusivities and the collective diffusivity of the ions.     

A light-gated synthetic ion channel

A gated synthetic ion channel with beta-cyclodextrin as the pore and azobenzene as the gate is reported. Irradiation converts a tethered trans-azobenzene to cis-azobenzene which likely transforms the channel from a self-inclusion complex to a dissociated structure. This transformation results in an increase in anion transport and a decrease in cation transport across a phospholipid vesicle membrane.     

Kinetic modeling of propane oxidation and pyrolysis

Propane oxidation in jet-stirred reactor was modeled using a comprehensive kinetic reaction mechanism including the most recent findings concerning the kinetics of the reactions involved in the oxidation of C₁? C₄ hydrocarbons. The present detailed mechanism is able to reproduce experimental species concentration profiles obtained in our high-pressure jet-stirred reactor (900 ? T/K ? 1200; 1 ? P/atm ? 10; 0.15 ? ? ? 4) and in a turbulent flow reactor at 1 atm; ignition delay times measured in shock tube (1200 ? T/K ? 1700; 2 ? P/atm ? 15; 0.125 ? ? ? 2); H-atoms concentrations measured in shock tube during the pyrolysis of propane and burning velocities of freely propagating premixed propane-air laminar flames. The computed results are discussed in terms of pressure and equivalence ratio (?) effects on propane oxidation. The same detailed kinetic reaction mechanism can also be used to model the oxidation of methane, ethylene, ethane, and propene in similar conditions. © John Wiley & Sons, Inc.     

Thermal decomposition of acetonitrile. Kinetic modeling

The thermal decomposition of acetonitrile in the temperature range 1350–1950 K is modeled with a reaction scheme containing 23 species and 43 elementary reactions. Values of {[product]_t/[CH₃CN]₀}/t, which were reported in a previous investigation are computed with this scheme at 50 K intervals and are compared with the values reported in the literature. Except for acrylonitrile and propyl nitrile at the high-temperature end of the study, very good agreement between the calculation and the experiment is obtained. A sensitivity spectrum of the kinetic scheme is shown and a discussion of the overall mechanism is presented. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 341–347, 1998     

Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site

Ion permeation through transmembrane channels has traditionally been modeled using two different approaches. In one approach, the translocation of the permeant ion through the channel pore is modeled as continuous diffusion and the rate of ion transport is obtained from solving the steady-state diffusion equation. In the other approach, the translocation of the permeant ion through the pore is modeled as hopping along a discrete set of internal binding sites and the rate of ion transport is obtained from solving a set of steady-state rate equations. In a recent work [Zhou, J. Phys. Chem. Lett. 1, 1973 (2010)], the rate constants for binding to an internal site were further calculated by modeling binding as diffusion-influenced reactions. That work provided the foundation for bridging the two approaches. Here we show that, by representing a binding site as an energy well, the two approaches indeed give the same result for the rate of ion transport.