An invertebrate glutamate-gated chloride channel (GluCl) has recently been crystallized in an open-pore state. This channel is homologous to the human Cys-loop receptor family of pentameric ...ligand-gated ion channels, including anion-selective GlyR and GABAR and cation-selective nAChR and 5HT3. We implemented molecular dynamics (MD) in conjunction with an elastic network model to perturb the X-ray structure of GluCl and investigated the open channel stability and its ion permeation characteristics. Our study suggests that TM2 helical tilting may close GluCl near the hydrophobic constriction L254 (L9′), similar to its cation-selective homologues. Ion permeation characteristics were determined by Brownian dynamics simulations using a hybrid MD/continuum electrostatics approach to evaluate the free energy profiles for ion transport. Near the selectivity filter region (P243 or P-2′), the free energy barrier for Na+ transport is over 4 k B T higher than that for Cl–, indicating anion selectivity of the channel. Furthermore, three layers of positivity charged rings in the extracellular domain also contribute to charge selectivity and facilitate Cl– permeability over Na+. Collectively, the charge selectivity of GluCl may be determined by overall electrostatic and ion dehydration effects, perhaps not deriving from a single region of the channel (the selectivity filter region near the intracellular entrance).
Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In ...the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na+ revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na+ was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl− was found to be 3−4 times higher than that for Na+. Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P Cl/P Na) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl− ions. The effect of halothane on the Na+ PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.
Calculation of Iron Transport through Human H‑chain Ferritin Laghaei, Rozita; Kowallis, William; Evans, Deborah G ...
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
09/2014, Letnik:
118, Številka:
35
Journal Article
Recenzirano
Influx of ferrous ions from the cytoplasm through 3-fold pores in the shell of ferritin protein is computed using a 3-dimensional Poisson–Nernst–Planck electrodiffusion model, with inputs such as the ...pore structure and the diffusivity profile of permeant Fe2+ ions extracted from all-atom molecular dynamics (MD) simulations. These calculations successfully reproduce experimental estimates of the transit time of Fe2+ through the ferritin coat, which is on the millisecond time scale and hence much too long to be directly simulated via all-atom MD. This is also much longer than the typical time scale for ion transit in standard membrane spanning ion channels whose pores bear structural similarity to that of the 3-fold ferritin pore. The slow time scale for Fe2+ transport through ferritin pores is traced to two features that distinguish the ferritin pore system from standard ion channels, namely, (i) very low concentration of cytoplasmic Fe2+ under physiological conditions and (ii) very small internal diffusion coefficients for ions inside the ferritin pore resulting from factors that include the divalent nature of Fe2+ and two rings of negatively charged amino acids surrounding a narrow geometric obstruction within the ferritin pore interior.
Analytical estimation of state-to-state rate constants is carried out for a recently developed discrete state model of chloride ion motion in a CLC chloride channel (Coalson and Cheng, J. Phys. Chem. ...B 2010, 114, 1424). In the original presentation of this model, the same rate constants were evaluated via three-dimensional Brownian dynamics simulations. The underlying dynamical theory is an appropriate single- or multiparticle three-dimensional Smoluchowski equation. Taking advantage of approximate geometric symmetries (based on the details of the model channel geometry), well-known formulas for state-to-state transition rates are appealed to herein and adapted as necessary to the problem at hand. Rates of ionic influx from a bulk electrolyte reservoir to the nearest binding site within the channel pore are particularly challenging to compute analytically because they reflect multi-ion interactions (as opposed to single-ion dynamics). A simple empirical correction factor is added to the single-ion rate constant formula in this case to account for the saturation of influx rate constants with increasing bulk Cl– concentration. Overall, the agreement between all analytically estimated rate constants is within a factor of 2 of those computed via three-dimensional Brownian dynamics simulations, and often better than this. Current–concentration curves obtained using rate constants derived from these two different computational approaches agree to within 25%.
Langevin dynamics is used to compute the time evolution of the nonequilibrium motion of the atomic coordinates of a protein in response to ligand dissociation. The protein potential energy surface ...(PES) is approximated by a harmonic basin about the minimum of the unliganded state. Upon ligand dissociation, the protein undergoes relaxation from the bound to the unbound state. A coarse graining scheme based on rotation translation blocks (RTB) is applied to the relaxation of the two domain iron transport protein, ferric binding protein. This scheme provides a natural and efficient way to freeze out the small amplitude, high frequency motions within each rigid fragment, thereby allowing for the number of dynamical degrees of freedom to be reduced. The results obtained from all flexible atom (constraint free) dynamics are compared to those obtained using RTB-Langevin dynamics. To assess the impact of the assumed rigid fragment clustering on the temporal relaxation dynamics of the protein molecule, three distinct rigid block decompositions were generated and their responses compared. Each of the decompositions was a variant of the one-block-per-residue grouping, with their force and friction matrices being derived from their fully flexible counterpart. Monitoring the time evolution of the distance separating a selected pair of amino acids, the response curves of the blocked decompositions were similar in shape to each other and to the control system in which all atomic degrees of freedom are fully independent. The similar shape of the blocked responses showed that the variations in grouping had only a minor impact on the kinematics. Compared with the all atom responses, however, the blocked responses were faster as a result of the instantaneous transmission of force throughout each rigid block. This occurred because rigid blocking does not permit any intrablock deformation that could store or divert energy. It was found, however, that this accelerated response could be successfully corrected by scaling each eigenvalue in the appropriate propagation matrix by the least-squares fitted slope of the blocked vs nonblocked eigenvalue spectra. The RTB responses for each test system were dominated by small eigenvalue overdamped Langevin modes. The large eigenvalue members of each response dissipated within the first 5 ps, after which the long time response was dominated by a modest set of low energy, overdamped normal modes, that were characterized by highly cooperative, functionally relevant displacements. The response assuming that the system is in the overdamped limit was compared to the full phase space Langevin dynamics results. The responses after the first 5 ps were nearly identical, confirming that the inertial components were significant only in the initial stages of the relaxation. Since the propagator matrix in the overdamped formulation is real-symmetric and does not require the inertial component in the propagator, the computation time and memory footprint was reduced by 1 order of magnitude.
A discrete-state model of chloride ion motion in a ClC chloride channel is constructed, following a previously developed multi-ion continuous space model of the same system (Cheng, M. H.; Mamonov, A. ...B.; Dukes, J. W.; Coalson, R. D. J. Phys. Chem. B 2007, 111, 5956) that included a simplistic representation of the fast gate in this channel. The reducibility of the many-body continuous space to the eight discrete-state model considered in the present work is examined in detail by performing three-dimensional Brownian dynamics simulations of each allowed state-to-state transition in order to extract the appropriate rate constant for this process, and then inserting the pairwise rate constants thereby obtained into an appropriate set of kinetic master equations. Experimental properties of interest, including the rate of Cl− ion permeation through the open channel and the average rate of closing of the fast gate as a function of bulk Cl− ion concentrations in the intracellular and extracellular electrolyte reservoirs are computed. Good agreement is found between the results obtained via the eight discrete-state model versus the multi-ion continuous space model, thereby encouraging continued development of the discrete-state model to include more complex behaviors observed experimentally in these channels.
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