Fantastic beasts and how to find them—Molecular identification of the mitochondrial ATP-sensitive potassium channel

Despite reported sightings over many years, certain mitochondrial-specific channels have proven to be elusive beasts, evading molecular identification. However, combining modern genetics with a wave of their ion-sensing wand, researchers have managed to capture first the mitochondrial calcium uniporter, and now that semi-mythological beast, the mitochondrial ATP-sensitive potassium (mitoK_ATP) channel.     

KCNK?: opening and closing the 2-P-domain potassium leak channel entails "C-type" gating of the outer pore.

Essential to nerve and muscle function, little is known about how potassium leak channels operate. KCNK? opens and closes in a kinase-dependent fashion. Here, the transition is shown to correspond to changes in the outer aspect of the ion conduction pore. Voltage-gated potassium (VGK) channels open and close via an internal gate; however, they also have an outer pore gate that produces "C-type" inactivation. While KCNK? does not inactivate, KCNK? and VGK channels respond in like manner to outer pore blockers, potassium, mutations, and chemical modifiers. Structural relatedness is confirmed: VGK residues that come close during C-type gating predict KCNK? sites that crosslink (after mutation to cysteine) to yield channels controlled by reduction and oxidization. We conclude that similar outer pore gates mediate KCNK? opening and closing and VGK channel C-type inactivation despite their divergent structures and physiological roles.     

Is the potassium channel distribution in glial cells optimal for spatial buffering of potassium?

Glial cells in the nervous system are believed to reduce changes of extracellular potassium concentration ([K+]o), caused by neural activity, by carrying out spatial buffering of potassium. In the case of retinal glial cells (Müller cells), light-evoked increases of [K+]o within the retina are reduced by K ions flowing through the Müller cell to the vitreous fluid of the eye. We have calculated the optimal way to distribute the potassium conductance of the Müller cell to maximize spatial buffering to the vitreous fluid. The best distribution is with half the potassium conductance in the outer part of the cell, where K+ enters, and half the conductance in the vitreal endfoot, where K+ leaves the cell. This calculated distribution is very different from the actual distribution measured by Newman (1984, Nature [Lond.], 309: 155-157), where only 6% of the Müller cell conductance is in the outer cell and 94% is in the endfoot. The experimentally observed distribution gives less than a quarter of the spatial buffering that would be produced by the optimal distribution. The possible advantages of this arrangement are discussed.     

Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1α

In all organisms, the large ribosomal subunit contains multiple copies of a flexible protein, the so-called ‘stalk’. The C-terminal domain (CTD) of the stalk interacts directly with the translational GTPase factors, and this interaction is required for factor-dependent activity on the ribosome. Here we have determined the structure of a complex of the CTD of the archaeal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1α at 2.3 Å resolution. The structure showed that the CTD of aP1 formed a long extended α-helix, which bound to a cleft between domains 1 and 3 of aEF1α, and bridged these domains. This binding between the CTD of aP1 and the aEF1α•GDP complex was formed mainly by hydrophobic interactions. The docking analysis showed that the CTD of aP1 can bind to aEF1α•GDP located on the ribosome. An additional biochemical assay demonstrated that the CTD of aP1 also bound to the aEF1α•GTP•aminoacyl-tRNA complex. These results suggest that the CTD of aP1 interacts with aEF1α at various stages in translation. Furthermore, phylogenetic perspectives and functional analyses suggested that the eukaryotic stalk protein also interacts directly with domains 1 and 3 of eEF1α, in a manner similar to the interaction of archaeal aP1 with aEF1α.     

Molecular simulation of polymers with a SAFT-γ Mie approach

ABSTRACT

We review the group contribution Statistical Associating Fluid Theory with Mie interaction potentials (SAFT-γ Mie) approach for building coarse-grained models for molecular simulation of polymeric systems. In this top-down method, force field parameters for coarse-grained polymer models can be derived from thermodynamic information on constituent monomer units using the SAFT-γ Mie equation of state (EoS). This strategy can facilitate high-throughput computational screening of polymeric materials, with a corresponding states correlation expediting the force field fitting. Accurate and transferable non-bonded parameters linked to macroscopic thermodynamic data allow for calculation of properties beyond those obtainable from the EoS alone. To overcome limitations of SAFT-γ Mie regarding polymer chain stiffness and branching, hybrid top-down/bottom-up approaches have combined non-bonded parameters from SAFT-γ Mie with bond-stretching and angle-bending potentials from higher-resolution force fields. Our review critically evaluates the performance of recent SAFT-γ Mie polymer models, highlighting the strengths and weaknesses in the context of other equation of state and coarse-graining methods.     

Molecular simulation of β-cyclodextrin inclusion complex with 2-phenylethyl alcohol

The structures of β-cyclodextrin inclusion complexes with 2-phenylethyl alcohol in vacuum and aqueous solution have been investigated by using molecular dynamics simulation. The inclusion structures and the physicochemical stability of the complexes were also analysed, discussed and validated by ultraviolet spectrums and thermodynamic properties. The results of molecular dynamics simulation indicate that the A-type β-cyclodextrin inclusion complex with 2-phenylethyl alcohol in both vacuum and aqueous solution have better physical stability, and its chemical stability also has obvious promotion than that of free one. Therefore, the β-cyclodextrin can be used to control and regulate the release of the 2-phenylethyl in food.     

Molecular architecture of the Dam1 complex–microtubule interaction

Mitosis is a highly regulated process that allows the equal distribution of the genetic material to the daughter cells. Chromosome segregation requires the formation of a bipolar mitotic spindle and assembly of a multi-protein structure termed the kinetochore to mediate attachments between condensed chromosomes and spindle microtubules. In budding yeast, a single microtubule attaches to each kinetochore, necessitating robustness and processivity of this kinetochore–microtubule attachment. The yeast kinetochore-localized Dam1 complex forms a direct interaction with the spindle microtubule. In vitro, the Dam1 complex assembles as a ring around microtubules and couples microtubule depolymerization with cargo movement. However, the subunit organization within the Dam1 complex, its higher-order oligomerization and how it interacts with microtubules remain under debate. Here, we used chemical cross-linking and mass spectrometry to define the architecture and subunit organization of the Dam1 complex. This work reveals that both the C termini of Duo1 and Dam1 subunits interact with the microtubule and are critical for microtubule binding of the Dam1 complex, placing Duo1 and Dam1 on the inside of the ring structure. Integrating this information with available structural data, we provide a coherent model for how the Dam1 complex self-assembles around microtubules.     

Molecular interaction of δ-conopeptide EVIA with voltage-gated Na+ channels

BackgroundFor a large number of conopeptides basic knowledge related to structure-activity relationships is unavailable although such information is indispensable with respect to drug development and their use as drug leads.MethodsA combined experimental and theoretical approach employing electrophysiology and molecular modeling was applied for identifying the conopeptide δ-EVIA binding site at voltage-gated Na⁺ channels and to gain insight into the toxin's mode of action.ResultsConopeptide δ-EVIA was synthesized and its structure was re-determined by NMR spectroscopy for molecular docking studies. Molecular docking and molecular dynamics simulation studies were performed involving the domain IV voltage sensor in a resting conformation and part of the domain I S5 transmembrane segment. Molecular modeling was stimulated by functional studies, which demonstrated the importance of domains I and IV of the neuronal Na_V1.7 channel for toxin action.Conclusionsδ-EVIA shares its binding epitope with other voltage-sensor toxins, such as the conotoxin δ-SVIE and various scorpion α-toxins. In contrast to previous in silico toxin binding studies, we present here in silico binding studies of a voltage-sensor toxin including the entire toxin binding site comprising the resting domain IV voltage sensor and S5 of domain I.General significanceThe prototypical voltage-sensor toxin δ-EVIA is suited for the elucidation of its binding epitope; in-depth analysis of its interaction with the channel target yields information on the mode of action and might also help to unravel the mechanism of voltage-dependent channel gating and coupling of activation and inactivation.     

Molecular simulation uncovers the conformational space of the λ Cro dimer in solution

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg⁴ and Glu⁵³ during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution.     

Molecular basis of the γ-aminobutyric acid A receptor α3 subunit interaction with the clustering protein gephyrin

The multifunctional scaffolding protein gephyrin is a key player in the formation of the postsynaptic scaffold at inhibitory synapses, clustering both inhibitory glycine receptors (GlyRs) and selected GABA(A) receptor (GABA(A)R) subtypes. We report a direct interaction between the GABA(A)R α3 subunit and gephyrin, mapping reciprocal binding sites using mutagenesis, overlay, and yeast two-hybrid assays. This analysis reveals that critical determinants of this interaction are located in the motif FNIVGTTYPI in the GABA(A)R α3 M3-M4 domain and the motif SMDKAFITVL at the N terminus of the gephyrin E domain. GABA(A)R α3 gephyrin binding-site mutants were unable to co-localize with endogenous gephyrin in transfected hippocampal neurons, despite being able to traffic to the cell membrane and form functional benzodiazepine-responsive GABA(A)Rs in recombinant systems. Interestingly, motifs responsible for interactions with GABA(A)R α2, GABA(A)R α3, and collybistin on gephyrin overlap. Curiously, two key residues (Asp-327 and Phe-330) in the GABA(A)R α2 and α3 binding sites on gephyrin also contribute to GlyR β subunit-E domain interactions. However, isothermal titration calorimetry reveals a 27-fold difference in the interaction strength between GABA(A)R α3 and GlyR β subunits with gephyrin with dissociation constants of 5.3 μm and 0.2 μm, respectively. Taken together, these observations suggest that clustering of GABA(A)R α2, α3, and GlyRs by gephyrin is mediated by distinct mechanisms at mixed glycinergic/GABAergic synapses.     

Crucial points within the pore as determinants of K⁺ channel conductance and gating

While selective for K⁺, K⁺ channels vary significantly among their rate of ion permeation. Here, we probe the effect of steric hindrance and electrostatics within the ion conduction pathway on K⁺ permeation in the MthK K⁺ channel using structure-based mutagenesis combined with single-channel electrophysiology and X-ray crystallography. We demonstrate that changes in side-chain size and polarity at Ala88, which forms the constriction point of the open MthK pore, have profound effects on single-channel conductance as well as open probability. We also reveal that the negatively charged Glu92s at the intracellular entrance of the open pore form an electrostatic trap, which stabilizes a hydrated K⁺ and facilitates ion permeation. This electrostatic attraction is also responsible for intracellular divalent blockage, which renders the channel inward rectified in the presence of Ca²⁺. In light of the high structural conservation of the selectivity filter, the size and chemical environment differences within the portion of the ion conduction pathway other than the filter are likely the determinants for the conductance variations among K⁺ channels.     

Structural determinants of the regulation of the voltage-gated potassium channel Kv2.1 by the modulatory α-subunit Kv9.3

Voltage-gated potassium (Kv) channels containing alpha-subunits of the Kv2 subfamily mediate delayed rectifier currents in excitable cells. Channels formed by Kv2.1 alpha-subunits inactivate from open- and closed states with both forms of inactivation serving different physiological functions. Here we show that open- and closed-state inactivation of Kv2.1 can be distinguished by the sensitivity to intracellular tetraethylammonium and extracellular potassium and lead to the same inactivated conformation. The functional properties of Kv2.1 are regulated by its association with modulatory alpha-subunits (Kv5, Kv6, Kv8, and Kv9). For instance, Kv9.3 changes the state preference of Kv2.1 inactivation by accelerating closed-state inactivation and inhibiting open-state inactivation. An N-terminal regulatory domain (NRD) has been suggested to determine the function of the modulatory alpha-subunit Kv8.1. However, when we tested the NRD of Kv9.3, we found that the functional properties of chimeric Kv2.1 channels containing the NRD of Kv9.3 (Kv2.1(NRD)) did not resemble those of Kv2.1/Kv9.3 heteromers, thus questioning the role of the NRD in Kv9 subunits. A further region of interest is a PXP motif in the sixth transmembrane segment. This motif is conserved among all alpha-subunits of the Kv1, Kv2, Kv3, and Kv4 subfamilies, whereas the second proline is not conserved in any modulatory alpha-subunit. Exchanging this proline in Kv2.1 for the corresponding residue of Kv9.3 resulted in channels (Kv2.1-P410T) that show all hallmarks of the regulation of Kv2.1 by Kv9.3. The effect prevailed in heteromeric channels following co-expression of Kv2.1-P410T with Kv2.1. These data suggest that the alteration of the PXP motif is an important determinant of the regulatory function of modulatory alpha-subunits.     

Computer simulation of the interaction of α3hclix of λ Cro protein with DNA and origin of sequence specific recognition

The conformation of the α3 helix of Cro protein (residues 27–36) of bacteriophageλ is optimised by the damped least square minimization technique, with the steric constraint that Cα atom positions should match the crystallographic data available to date. On the basis of minimization of total interaction and conformation energy, models for complexes of this peptide sequence with heptanucleotide duplexes from native and altered O_R3 operator are obtained in the major groove of B DNA. Analysis of the energetics for 3 sequences of the DNA show that binding strength is derived mainly from the interaction of side chains of the peptide with DNA. Sequence specificity (maximum difference in binding energy for different DNA sequences) is due to hydrogen bonding interaction. A small amount of sequence specificity is derived from non-bonded interaction also. Stereochemical aspects of peptide DNA interaction and their role in DNA recognition are discussed in this paper.     

Enhancement of TREK1 channel surface expression by protein-protein interaction with β-COP

TREK1 belongs to a family of two-pore-domain K⁺ (K_2P) channels and produce background currents that regulate cell excitability. In the present study, we identified a vesicle transport protein, β-COP, as an interacting partner by yeast two-hybrid screening of a human brain cDNA library with N-terminal region of TREK1 (TREK1-N) as bait. Several in vitro and in vivo binding assays confirmed the protein-protein interaction between TREK1 and β-COP. We also found that β-COP was associated with TREK1 in native condition at the PC3 cells. When RFP-β-COP was co-transfected with GFP-TREK1 into COS-7 cells, both proteins were found localized to the plasma membrane. In addition, the channel activity and surface expression of GFP-TREK1 increased dramatically by co-transfection with RFP-β-COP. Surface expression of the TREK1 channel was also clearly reduced with the addition of β-COP-specific shRNA. Collectively, these data suggest that β-COP plays a critical role in the forward transport of TREK1 channel to the plasma membrane.     

Carboxy-terminal domain mediates assembly of the voltage-gated rat ether-à-go-go potassium channel.

The specific assembly of subunits to oligomers is an important prerequisite for producing functional potassium channels. We have studied the assembly of voltage-gated rat ether-à-go-go (r-eag) potassium channels with two complementary assays. In protein overlay binding experiments it was shown that a 41-amino-acid domain, close to the r-eag subunit carboxy-terminus, is important for r-eag subunit interaction. In an in vitro expression system it was demonstrated that r-eag subunits lacking this assembly domain cannot form functional potassium channels. Also, a approximately 10-fold molar excess of the r-eag carboxy-terminus inhibited in co-expression experiments the formation of functional r-eag channels. When the r-eag carboxy-terminal assembly domain had been mutated, the dominant-negative effect of the r-eag carboxy-terminus on r-eag channel expression was abolished. The results demonstrate that a carboxy-terminal assembly domain is essential for functional r-eag potassium channel expression, in contrast to the one of Shaker-related potassium channels, which is directed by an amino-terminal assembly domain.     

The interaction of “K+-like” cations with the apical K+ channel in frog skin

The apparent permeability of the apical K+ channel in the abdominal skin of the frog (Rana temporaria) for different monovalent cations was tested by comparing the short-circuit current (SCC) obtained after imposition of serosally directed ionic concentration gradients. Furthermore, the SCC was subjected to noise analysis. Of various cations tested, only the "K+-like" ions NH+4, Rb+ and Tl+, besides K+, were found to permeate the apical K+ channel, as reflected by SCC- and fluctuation analysis: (i) The SCC could be depressed by addition of the K+-channel blocker Ba2+ to the mucosal solution. (ii) With the K+-like ions (Ringer's concentration), a spontaneous Lorentzian noise was observed. Plateau values were similar for K+ and Tl+, and smaller for NH+4 and Rb+. The corner frequencies clearly increased in the order K+ less than NH+4 less than Tl+ much less than Rb+. The SCC dose-response relationships revealed a Michaelis-Menten-type current saturation only for pure K+- or Tl+-Ringer's solutions as mucosal medium, whereas a more complicated SCC behavior was seen with Rb+ and especially, NH+4. For K+-Tl+ mixtures an anomalous mole-fraction relationship was observed: At low [Tl+]/[K+] ratios, Tl+ ions appeared to inhibit competitively the K+ current while, at high [Tl+]/[K+] ratios, Tl+ seemed to be a permeant cation. This feature was also detected in the noise analysis of K+-Tl+ mixtures. Long-term exposure to mucosal Tl+ resulted in an irreversible deterioration of the tissue. The SCC depression by Ba2+ was of a simple saturation-type characteristic with, however, different half-maximal doses (NH+4 less than K+ less than Rb+). Ba2+ induced a "blocker noise" in presence of all permeant cations with corner frequencies that depended on the Ba2+ concentration. A linear increase of the corner frequencies of the Ba2+-induced noise with increasing Ba2+ concentration was seen for NH+4, Rb+ and K+. With the assumption of a pseudo two-state model for the Ba2+ blockade the on- and off-rate constants for the Ba2+ interaction with the NH+4/Rb+/K+ channel were calculated and showed marked differences, dependent on the nature of the permeant ion. The specific problems with Tl+ prevented such an analysis but SCC- and noise data indicated a comparably poor efficiency of Ba2+ as Tl+-current inhibitor. We attempted a qualitative analysis of our results in terms of a "two-sites, three-barriers" model of the apical K+ channel in frog skin.     

Molecular dynamics simulation of the melting processes of core–shell and pure nanoparticles

Core–shell nanoparticles are nanosized particles that consist of a core and a shell, constructed from different metallic elements. Core–shell nanoparticles have received extensive attention, owing to their various potential applications such as paints, optical films and catalysts. Herein, we investigate the melting behaviours of different core–shell nanoparticles under continuous heating using molecular dynamics simulation. Different metallic elements were examined as core–shell and pure nanoparticles. Five different processes were observed during the melting of core–shell nanoparticles. In contrast, only one process was identified during the melting of pure nanoparticles. These processes were influenced by the nanoparticle size, shell thickness and differences between the lattice constants and melting point temperatures of the metallic elements. Our simulation provides microscopic insights into the melting behaviours of existing and proposed core–shell nanoparticles that would be highly beneficial towards the fabrication of materials with different chemical coatings.     

Molecular docking and dynamics simulations on the interaction of cationic porphyrin–anthraquinone hybrids with DNA G-quadruplexes

A series of cationic porphyrin–anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.