Molecular dynamics simulations of migration of ions and molecules through the acetylcholine receptor channel

A dynamic model of the channel of an acetylcholine receptor in a closed state has been proposed. The channel is formed by five a-helices of subunit M2 and stabilized by the cyclic hydrocarbon (CH2)105. The migration of charged and unchanged van der Waals particles with a diameter of 7.72 A equivalent to the diameter of a hydrated sodium ion has been studied. The migration occurred by the action of external force applied to the complex along the channel axis. In the closed state, the inhibition of ions is due to two components: electrostatic interaction and steric constraints. The van der Waals channel gate is formed by residues 13'-A-Val255, B-Val261, C-Val269, D-Val255, and E-Ile264, and the negatively changed residues occurring in the upper part of the channel have a great effect on ion selectivity.     

Ion channel gates: comparative analysis of energy barriers

The energetic profile of an ion translated along the axis of an ion channel should reveal whether the structure corresponds to a functionally open or closed state of the channel. In this study, we explore the combined use of Poisson–Boltzmann electrostatic calculations and evaluation of van der Waals interactions between ion and pore to provide an initial appraisal of the gating state of a channel. This approach is exemplified by its application to the bacterial inward rectifier potassium channel KirBac3.1, where it reveals the closed gate to be formed by a ring of leucine (L124) side chains. We have extended this analysis to a comparative survey of gating profiles, including model hydrophobic nanopores, the nicotinic acetylcholine receptor, and a number of potassium channel structures and models. This enables us to identify three gating regimes, and to show the limitation of this computationally inexpensive method. For a (closed) gate radius of 0.4 nm < R < 0.8 nm, a hydrophobic gate may be present. For a gate radius of 0.2 nm < R < 0.4 nm, both electrostatic and van der Waals interactions will contribute to the barrier height. Below R = 0.2 nm, repulsive van der Waals interactions are likely to dominate, resulting in a sterically occluded gate. In general, the method is more useful when the channel is wider; for narrower channels, the flexibility of the protein may allow otherwise-unsurmountable energetic barriers to be overcome.     

Measuring electrostatic, van der Waals, and hydration forces in electrolyte solutions with an atomic force microscope

In atomic force microscopy, the tip experiences electrostatic, van der Waals, and hydration forces when imaging in electrolyte solution above a charged surface. To study the electrostatic interaction force vs distance, curves were recorded at different salt concentrations and pH values. This was done with tips bearing surface charges of different sign and magnitude (silicon nitride, Al₂O₃, glass, and diamond) on negatively charged surfaces (mica and glass). In addition to the van der Waals attraction, neutral and negatively charged tips experienced a repulsive force. This repulsive force depended on the salt concentration. It decayed exponentially with distance having a decay length similar to the Debye length. Typical forces were about 0.1 nN strong. With positively charged tips, purely attractive forces were observed. Comparing these results with calculations showed the electrostatic origin of this force.

In the presence of high concentrations (> 3 M) of divalent cations, where the electrostatic force can be completely ignored, another repulsive force was observed with silicon nitride tips on mica. This force decayed roughly exponentially with a decay length of 3 nm and was ~0.07-nN strong. This repulsion is attributed to the hydration force.

     

Identification of amino acid residues lining the pore of a gap junction channel

Gap junctions represent a ubiquitous and integral part of multicellular organisms, providing the only conduit for direct exchange of nutrients, messengers and ions between neighboring cells. However, at the molecular level we have limited knowledge of their endogenous permeants and selectivity features. By probing the accessibility of systematically substituted cysteine residues to thiol blockers (a technique called SCAM), we have identified the pore-lining residues of a gap junction channel composed of Cx32. Analysis of 45 sites in perfused Xenopus oocyte pairs defined M3 as the major pore-lining helix, with M2 (open state) or M1 (closed state) also contributing to the wider cytoplasmic opening of the channel. Additional mapping of a close association between M3 and M4 allowed the helices of the low resolution map (Unger et al., 1999. Science. 283:1176-1180) to be tentatively assigned to the connexin transmembrane domains. Contrary to previous conceptions of the gap junction channel, the residues lining the pore are largely hydrophobic. This indicates that the selective permeabilities of this unique channel class may result from novel mechanisms, including complex van der Waals interactions of permeants with the pore wall, rather than mechanisms involving fixed charges or chelation chemistry as reported for other ion channels.     

Glycan structures and antiviral effect of the structural subunit RvH2 of Rapana hemocyanin

Molluscan hemocyanins are very large biological macromolecules and they act as oxygen-transporting glycoproteins. Most of them are glycoproteins with molecular mass around 9000 kDa. The oligosaccharide structures of the structural subunit RvH2 of Rapana venosa hemocyanin (RvH) were studied by sequence analysis of glycans using MALDI-TOF-MS and tandem mass spectrometry on a Q-Trap mass spectrometer after enzymatical liberation of the N-glycans from the polypeptides. Our study revealed a highly heterogeneous mixture of glycans of the compositions Hex_0-9 HexNAc_2-4 Hex_0-3 Pent_0-3 Fuc_0-3. A novel type of N-glycan, with an internal fucose residue connecting one GalNAc(β1-2) and one hexuronic acid, was detected, as also occurs in subunit RvH1. A glycan with the same structure but with two deoxyhexose residues was observed as a doubly charged ion. Antiviral effects of the native molecules of RvH and also of Helix lucorum hemocyanin (HlH), of their structural subunits, and of the glycosylated functional unit RvH2-e and the non-glycosylated unit RvH2-c on HSV virus type 1 were investigated. Only glycosylated FU RvH2-e exhibits this antiviral activity. The carbohydrate chains of the FU are likely to interact with specific regions of glycoproteins of HSV, through van der Waals interactions in general or with certain amino acid residues in particular. Several clusters of these residues can be identified on the surface of RvH2-e.     

Tricyclic antidepressants and mecamylamine bind to different sites in the human α4β2 nicotinic receptor ion channel

The interaction of tricyclic antidepressants with the human (h) α4β2 nicotinic acetylcholine receptor in different conformational states was compared with that for the noncompetitive antagonist mecamylamine by using functional and structural approaches. The results established that: (a) [³H]imipramine binds to hα4β2 receptors with relatively high affinity (K_d = 0.83 ± 0.08 μM), but imipramine does not differentiate between the desensitized and resting states, (b) although tricyclic antidepressants inhibit (±)-epibatidine-induced Ca²⁺ influx in HEK293-hα4β2 cells with potencies that are in the same concentration range as that for (±)-mecamylamine, tricyclic antidepressants inhibit [³H]imipramine binding to hα4β2 receptors with affinities >100-fold higher than that for (±)-mecamylamine. This can be explained by our docking results where imipramine interacts with the leucine (position 9′) and valine (position 13′) rings by van der Waals contacts, whereas mecamylamine interacts electrostatically with the outer ring (position 20′), (c) van der Waals interactions are in agreement with the thermodynamic results, indicating that imipramine interacts with the desensitized and resting receptors by a combination of enthalpic and entropic components. However, the entropic component is more important in the desensitized state, suggesting local conformational changes. In conclusion, our data indicate that tricyclic antidepressants and mecamylamine efficiently inhibit the ion channel by interacting at different luminal sites. The high proportion of protonated mecamylamine calculated at physiological pH suggests that this drug can be attracted to the channel mouth before binding deeper within the receptor ion channel finally blocking ion flux.     

Molecular coupling in the human ether-a-go-go-related gene-1 (hERG1) K+ channel inactivation pathway

Emerging evidence suggests that K(+) channel inactivation involves coupling between residues in adjacent regions of the channel. Human ether-a-go-go-related gene-1 (hERG1) K(+) channels undergo a fast inactivation gating process that is crucial for maintaining electrical stability in the heart. The molecular mechanisms that drive inactivation in hERG1 channels are unknown. Using alanine scanning mutagenesis, we show that a pore helix residue (Thr-618) that points toward the S5 segment is critical for normal inactivation gating. Amino acid substitutions at position 618 modulate the free energy of inactivation gating, causing enhanced or reduced inactivation. Mutation of an S5 residue that is predicted to be adjacent to Thr-618 (W568L) abolishes inactivation and alters ion selectivity. The introduction of the Thr-618-equivalent residue in Kv1.5 enhances inactivation. Molecular dynamic simulations of the Kv1.2 tetramer reveal van der Waals coupling between hERG1 618- and 568-equivalent residues and a significant increase in interaction energies when threonine is introduced at the 618-equivalent position. We propose that coupling between the S5 segment and pore helix may participate in the inactivation process in hERG1 channels.     

The stacking of chloroplast thylakoids: Quantitative analysis of the balance of forces between thylakoid membranes of chloroplasts,and the role of divalent cations

An analysis is made of the van der Waals dispersion attractive forces and electrostatic repulsive forces between the grana thylakoid membranes of chloroplasts. These forces are determined for negatively charged surfaces with a pK_a value of 4.7 for a bulk pH of 7.0 with a range of mono- and divalent cation concentrations and intermembrane spacing in the range 10 to 80 Å. For equilibrium under dark conditions, it is concluded that either there is extensive electrostatic binding of divalent cations (Mg²⁺) to the negatively charged membrane groups (phospholipid, sulfolipid, and protein carboxyl), or a redistribution of these groups between stacked and unstacked regions must be invoked.     

Nature of Novel 2D van der Waals Heterostructures for Superior Potassium Ion Batteries

Novel 2D van der Waals heterostructures with innovative bimetallic oxychloride (Bi‐ and Sb‐based oxychloride) nanosheets that are well dispersed on reduced graphene oxide nanosheets, are established through element engineering for superior potassium ion battery (PIBs) anodes. This material displays an exceptional electrochemical performance, obtaining a discharge capacity as high as 360 mAh g^?1 at 100 mA g^?1 after running 1000 cycles for over 9 months with a capacity preservation percentage of 88.5% and achieving a discharge capacity as high as 319 mAh g^?1 at 1000 mA g^?1, in addition to the low charge/discharge plateaus for anodes and promising full cell performance. More significantly, the nature of such 2D van der Waals heterostructures, including the element engineering for morphology control, the function of each component of heterostructures, the mechanism of potassium ion storage, and the process of K⁺ intercalation accompanied with the lattice distortion and chemical bond breakages, is explored in depth. This study is critical for not only paving the way for the practical application of PIBs but also shedding light on fundamentals of potassium ion storage in 2D van der Waals heterostructures.     

Functional Analysis of the Kv1.1 N255D Mutation Associated with Autosomal Dominant Hypomagnesemia

Mutations in the voltage-gated K⁺ channel Kv1.1 have been linked with a mixed phenotype of episodic ataxia and/or myokymia. Recently, we presented autosomal dominant hypomagnesemia as a new phenotypic characteristic associated with a mutation in Kv1.1 (N255D) (Glaudemans, B., van der Wijst, J., Scola, R. H., Lorenzoni, P. J., Heister, A., van der Kemp, A. W., Knoers, N. V., Hoenderop, J. G., and Bindels, R. J. (2009) J. Clin. Invest. 119, 936–942). A conserved asparagine at position 255 in the third transmembrane segment was converted into an aspartic acid, resulting in a non-functional channel. In this study, we explored the functional consequence of this conserved residue by substitution with other hydrophobic, polar, or charged amino acids (N255E, N255Q, N255A, N255V, N255T, and N255H). Upon overexpression in human embryonic kidney (HEK293) cells, cell surface biotinylation revealed plasma membrane expression of all mutant channels. Next, we used the whole-cell patch clamp technique to demonstrate that the N255E and N255Q mutants were non-functional. Substitution of Asn-255 with other amino acids (N255A, N255V, N255T, and N255H) did not prevent ion conduction, and these mutant channels activated at more negative potentials when compared with wild-type channels, −41.5 ± 1.6, −45.5 ± 2.0, −50.5 ± 1.9, and −33.8 ± 1.3 mV to −29.4 ± 1.1 mV, respectively. The time constant of activation was significantly faster for the two most hydrophobic mutations, N255A (6.2 ± 0.2 ms) and N255V (5.2 ± 0.3 ms), and the hydrophilic mutant N255T (9.8 ± 0.4 ms) in comparison with wild type (13.0 ± 0.9 ms). Furthermore, the voltage dependence of inactivation was shifted ∼13 mV to more negative potentials in all mutant channels except for N255H. Taken together, our data showed that an asparagine at position 255 in Kv1.1 is required for normal voltage dependence and kinetics of channel gating.     

Role of hydrophobic and ionic forces in the movement of S4 of the Shaker potassium channel

Abstract

Voltage-gated ion (K⁺, Na⁺, Ca²⁺) channels contain a pore domain (PD) surrounded by four voltage sensing domains (VSD). Each VSD is made up of four transmembrane helices, S1–S4. S4 contains 6–7 positively charged residues (arginine/lysine) separated two hydrophobic residues, whereas S1–S3 contribute to two negatively charged clusters. These structures are conserved among all members of the voltage-gated ion channel family and play essential roles in voltage gating. The role of S4 charged residues in voltage gating is well established: During depolarization, they move out of the membrane electric field, exerting a mechanical force on channel gates, causing them to open. However, the role of the intervening hydrophobic residues in voltage sensing is unclear. Here we studied the role of these residues in the prototypical Shaker potassium channel. We have altered the physicochemical properties of both charged and hydrophobic positions of S4 and examined the effect of these modifications on the gating properties of the channel. For this, we have introduced cysteines at each of these positions, expressed the mutants in Xenopus oocytes, and examined the effect of in situ addition of charge, via Cd²⁺, on channel gating by two-electrode voltage clamp. Our results reveal a face of the S4 helix (comprising residues L358, L361, R365 and R368) where introduction of charge at hydrophobic positions destabilises the closed state and removal of charges from charged positions has an opposite effect. We propose that hydrophobic residues play a crucial role in limiting gating to a physiological voltage range.     

Regulation of channel function due to physical energetic coupling with a lipid bilayer

Regulation of membrane protein functions due to hydrophobic coupling with a lipid bilayer has been investigated. An energy formula describing interactions between lipid bilayer and integral ion channels with different structures, which is based on the screened Coulomb interaction approximation, has been developed. Here the interaction energy is represented as being due to charge-based interactions between channel and lipid bilayer. The hydrophobic bilayer thickness channel length mismatch is found to induce channel destabilization exponentially while negative lipid curvature linearly. Experimental parameters related to channel dynamics are consistent with theoretical predictions. To measure comparable energy parameters directly in the system and to elucidate the mechanism at an atomistic level we performed molecular dynamics (MD) simulations of the ion channel forming peptide–lipid complexes. MD simulations indicate that peptides and lipids experience electrostatic and van der Waals interactions for short period of time when found within each other’s proximity. The energies from these two interactions are found to be similar to the energies derived theoretically using the screened Coulomb and the van der Waals interactions between peptides (in ion channel) and lipids (in lipid bilayer) due to mainly their charge properties. The results of in silico MD studies taken together with experimental observable parameters and theoretical energetic predictions suggest that the peptides induce ion channels inside lipid membranes due to peptide–lipid physical interactions. This study provides a new insight helping better understand of the underlying mechanisms of membrane protein functions in cell membrane leading to important biological implications.     

Computational studies of gramicidin permeation: An entryway sulfonate enhances cation occupancy at entry sites

The impact on the cation-transport free-energy profile of replacing the C-terminal ethanolamine in the gramicidin A channel with a taurine residue is studied using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl saline solution. The potential of mean force for ion transport is obtained by umbrella sampling. The presence of a negatively charged sulfonate group at the entrance of the gramicidin channel affects the depth and the location of the binding sites, producing a strong attraction for the cations in the bulk. The potential of mean force by the sulfonate acting directly through electrostatics and van der Waals interactions on the test ion is highly modulated by indirect effects (i.e., sulfonate effects on other components of the system that, in turn, affect the ion free-energy profile in the channel). Because the “entry” sites are located symmetrically at both entry and exit of the channel, the deeper free-energy wells should inhibit exit. Given that the channel has increased conductance experimentally, the simulation results suggest that the channel conductance is normally entry limited.     

Unveiling the Unique Phase Transformation Behavior and Sodiation Kinetics of 1D van der Waals Sb2S3 Anodes for Sodium Ion Batteries

Carbon‐coated van der Waals stacked Sb₂S₃ nanorods (SSNR/C) are synthesized by facile hydrothermal growth as anodes for sodium ion batteries (SIBs). The sodiation kinetics and phase evolution behavior of the SSNR/C anode during the first and subsequent cycles are unraveled by coupling in situ transmission electron microscopy analysis with first‐principles calculations. During the first sodiation process, Na⁺ ions intercalate into the Sb₂S₃ crystals with an ultrafast speed of 146 nm s^?1. The resulting amorphous Na_x Sb₂S₃ intermediate phases undergo sequential conversion and alloying reactions to form crystalline Na₂S, Na₃Sb, and minor metallic Sb. Upon desodiation, Na⁺ ions extract from the nanocrystalline phases to leave behind the fully desodiated Sb₂S₃ in an amorphous state. Such unique phase evolution behavior gives rise to superb electrochemical performance and leads to an unexpectedly small volume expansion of ≈54%. The first‐principles calculations reveal distinctive phase evolution arising from the synergy between the extremely low Na⁺ ion diffusion barrier of 190 meV and the sharply increased electronic conductivity upon the formation of amorphous Na_x Sb₂S₃ intermediate phases. These findings highlight an anomalous Na⁺ ion storage mechanism and shed new light on the development of high performance SIB anodes based on van der Waals crystals.     

Molecular Dynamics Simulations Reveal the HIV-1 Vpu Transmembrane Protein to Form Stable Pentamers

The human immunodeficiency virus type I (HIV-1) Vpu protein is 81 residues long and has two cytoplasmic and one transmembrane (TM) helical domains. The TM domain oligomerizes to form a monovalent cation selective ion channel and facilitates viral release from host cells. Exactly how many TM domains oligomerize to form the pore is still not understood, with experimental studies indicating the existence of a variety of oligomerization states. In this study, molecular dynamics (MD) simulations were performed to investigate the propensity of the Vpu TM domain to exist in tetrameric, pentameric, and hexameric forms. Starting with an idealized α-helical representation of the TM domain, a thorough search for the possible orientations of the monomer units within each oligomeric form was carried out using replica-exchange MD simulations in an implicit membrane environment. Extensive simulations in a fully hydrated lipid bilayer environment on representative structures obtained from the above approach showed the pentamer to be the most stable oligomeric state, with interhelical van der Waals interactions being critical for stability of the pentamer. Atomic details of the factors responsible for stable pentamer structures are presented. The structural features of the pentamer models are consistent with existing experimental information on the ion channel activity, existence of a kink around the Ile17, and the location of tetherin binding residues. Ser23 is proposed to play an important role in ion channel activity of Vpu and possibly in virus propagation.     

The switch of the binding behaviours between Xe and π system induced by the change of oxidation state of Cu ion

Abstract

The interaction between a xenon atom and aromatic π electron system is generally of van der Waals force with a specifically weak strength. In this work, we suggest the introduction of Cu ion will highly affect the binding behaviour between the xenon and π systems. Once Cu²⁺ ion locates above the benzene ring, the binding is surprisingly strengthened to 11.98 kcal mol^?1 at CCSD(T)/CBS level, which is significantly stronger than average strength of the H-bonds in Watson-Crick guanine-cytosine base pair. If the Cu²⁺ is reduced to Cu⁺, the interaction of interest returns to the weak van der Waals interaction again. This phenomenon indicates the oxidation state shift of Cu ion could regulate the binding strength of Xe with π systems, which would be important for their potential biological functions. This study may provide a plausible understanding of the recent experimental observations of xenon anaesthesia.     

Interfacial gating triad is crucial for electromechanical transduction in voltage-activated potassium channels

Voltage-dependent potassium channels play a crucial role in electrical excitability and cellular signaling by regulating potassium ion flux across membranes. Movement of charged residues in the voltage-sensing domain leads to a series of conformational changes that culminate in channel opening in response to changes in membrane potential. However, the molecular machinery that relays these conformational changes from voltage sensor to the pore is not well understood. Here we use generalized interaction-energy analysis (GIA) to estimate the strength of site-specific interactions between amino acid residues putatively involved in the electromechanical coupling of the voltage sensor and pore in the outwardly rectifying K_V channel. We identified candidate interactors at the interface between the S4–S5 linker and the pore domain using a structure-guided graph theoretical approach that revealed clusters of conserved and closely packed residues. One such cluster, located at the intracellular intersubunit interface, comprises three residues (arginine 394, glutamate 395, and tyrosine 485) that interact with each other. The calculated interaction energies were 3–5 kcal, which is especially notable given that the net free-energy change during activation of the Shaker K_V channel is ∼14 kcal. We find that this triad is delicately maintained by balance of interactions that are responsible for structural integrity of the intersubunit interface while maintaining sufficient flexibility at a critical gating hinge for optimal transmission of force to the pore gate.     

Ion channels formed by amphipathic helical peptides

Channel forming peptides (CFPs) are amphipathic peptides, of length ca. 20 residues, which adopt an -helical conformation in the presence of lipid bilayers and form ion channels with electrophysiological properties comparable to those of ion channel proteins. We have modelled CFP channels as bundles of parallel trans-bilayer helices surrounding a central ion-permeable pore. Ion-channel interactions have been explored via accessible surface area calculations, and via evaluation of changes in van der Waals and electrostatic energies as a K⁺ ion is translated along the length of the pore. Two CFPs have been modelled: (a) zervamicin-A1-16, a synthetic apolar peptaibol related to alamethicin, and (b) -toxin from Staphylococcus aureus. Both of these CFPs have previously been shown to form ion channels in planar lipid bilayers, and have been shown to have predominantly helical conformations. Zervamicin-A1-16 channels were modelled as bundles of 4 to 8 parallel helices. Two related helix bundle geometries were explored. K⁺channel interactions have been shown to involve exposed backbone carbonyl oxygen atoms. -Toxin channels were modelled as bundles of 6 parallel helices. Residues Q3, D11 and D18 generate favourable K⁺-channel interactions. Rotation of W15 about its C-C bond has been shown to be capable of occluding the central pore, and is discussed as a possible model for sidechain conformational changes in relation to ion channel gating.     

Influence of cation-pi interactions in different folding types of membrane proteins

Cation-pi interactions play an important role to the stability of protein structures. In this work, we analyze the influence of cation-pi interactions in three-dimensional structures of membrane proteins. We found that transmembrane strand (TMS) proteins have more number of cation-pi interactions than transmembrane helical (TMH) proteins. In TMH proteins, both the positively charged residues Lys and Arg equally experience favorable cation-pi interactions whereas in TMS proteins, Arg is more likely than Lys to be in such interactions. There is no relationship between number of cation-pi interactions and number of residues in TMH proteins whereas a good correlation was observed in TMS proteins. The average cation-pi interaction energy for TMH proteins is -16 kcal/mol and that for TMS proteins is -27 kcal/mol. The pair-wise cation-pi interaction energy between aromatic and positively charged residues showed that Lys-Trp energy is stronger in TMS proteins than TMH proteins; Arg-Phe, Arg-Tyr and Lys-Phe have higher energy in TMH proteins than TMS proteins. The decomposition of energies into electrostatic and van der Waals revealed that the contribution from electrostatic energy is twice as that from van der Waals energy in both TMH and TMS proteins. The results obtained in the present study would be helpful to understand the contribution of cation-pi interactions to the stability of membrane proteins.     

The impact of <Emphasis Type="Italic">Trichoderma reesei</Emphasis> Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study

A critical role of the Family 7 cellobiohydrolase (Cel7A) carbohydrate binding domain (CBD) is to bind to a cellulose surface and increase the enzyme concentration on the surface. Several residues of Trichoderma reesei Cel7A CBD, including Y5, N29, Y31, Y32 and Q34, contribute to cellulose binding, as revealed by early experimental studies. To investigate the interactions between these important residues and cellulose, we applied a thermodynamic integration method to calculate the cellulose–Cel7A CBD binding free energy changes caused by Y5A, N29A, Y31A, Y32A and Q34A mutations. The experimental binding trend was successfully predicted, proving the effectiveness of the complex model. For the two polar residue mutants N29A and Q34A, the changes in the electrostatics are comparable to those of van der Waals, while for three Y to A mutants, the free energy differences mainly come from van der Waals interactions. However, in both cases, the electrostatics dominates the interactions between individual residues and cellulose. The side chains of these residues are rigidified after the complex is formed. The binding free energy changes for the two mutants Y5W and Y31W were also determined, and for these the van der Waals interaction was strengthened but the electrostatics was weakened.