Ion Permeation in the NanC Porin from Escherichia coli: Free Energy Calculations along Pathways Identified by Coarse-Grain Simulations (original) (raw)
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A 5 ns all-atom molecular dynamics trajectory of Escherichia coli OmpF porin embedded in an explicit dimyristoyl-phosphatidylcholine (DMPC) bilayer bathed by a 1 M [KCl] aqueous salt solution is generated to explore the microscopic details of the mechanism of ion permeation. The atomic model includes the OmpF trimer, 124 DMPC, 13470 water molecules as well as 231 K þ and 201 Cl 2 , for a total of 70,693 atoms. The structural and dynamical results are in excellent agreement with the X-ray data. The global root-mean-square deviation of the backbone atoms relative to the X-ray structure is 1.4 Å . A cluster of three fully charged arginine (Arg42, Arg82, and Arg132) facing two acidic residues (Asp113 and Glu117) on L3 in the narrowest part of the aqueous pore is observed to be very stable in the crystallographic conformation. In this region of the pore, the water molecules are markedly oriented perpendicular to the channel axis due to the strong transversal electrostatic field arising from those residues. On average the size of the pore is smaller during the simulation than in the X-ray structure, undergoing small fluctuations. No large movements of loop L3 leading to a gating of the pore are observed. Remarkably, it is observed that K þ and Cl 2 follow two well-separated average pathways spanning over nearly 40 Å along the axis of the pore. In the center of the monomer, the two screw-like pathways have a lefthanded twist, undergoing a counter-clockwise rotation of 1808 from the extracellular vestibule to the pore periplasmic side. In the pore, the dynamical diffusion constants of the ions are reduced by about 50% relative to their value in bulk solvent. Analysis of ion solvation across the channel reveals that the contributions from the water and the protein are complementary, keeping the total solvation number of both ions nearly constant. Unsurprisingly, K þ have a higher propensity to occupy the aqueous pore than Cl 2 , consistent with the cation selectivity of the channel. However, further analysis suggests that ion -ion pairs play an important role. In particular, it is observed that the passage of Cl 2 occurs only in the presence of K þ counterions, and isolated K þ can move through the channel and permeate on their own. The presence of K þ in the pore screens the negative electrostatic potential arising from OmpF to help the translocation of Cl 2 by formation of ion pairs.
Journal of Chemical Physics, 2014
Chloride anions permeate the bacterial NanC porin in physiological processes. Here we present a DFT-based QM/MM study of this porin in the presence of these anions. Comparison is made with classical MD simulations on the same system. In both QM/MM and classical approaches, the anions are almost entirely solvated by water molecules. However, the average water-Cl − distance is significantly larger in the first approach. Polarization effects of protein groups close to Cl − anion are sizeable. These effects might modulate the anion-protein electrostatic interactions, which in turn play a central role for selectivity mechanisms of the channel.
The Journal of Chemical Physics, 2014
Chloride anions permeate the bacterial NanC porin in physiological processes. Here we present a DFT-based QM/MM study of this porin in the presence of these anions. Comparison is made with classical MD simulations on the same system. In both QM/MM and classical approaches, the anions are almost entirely solvated by water molecules. However, the average water-Cl − distance is significantly larger in the first approach. Polarization effects of protein groups close to Cl − anion are sizeable. These effects might modulate the anion-protein electrostatic interactions, which in turn play a central role for selectivity mechanisms of the channel.
Physical Review E, 2011
We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force Feff can be obtained after appropriate subdivison of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson-Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.
Biophysical Journal, 2011
We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed several first passage time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous, description in terms of a constant diffusion coefficient D and an effective deterministic force F eff can be obtained after appropriate subdivison of the channel in different regions suggested by the X-ray structure. These results have important implications for popular simplified descriptions of channels based on the 1D Poisson-Nernst-Planck (PNP) equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.
Biophysical Journal, 2010
We performed all-atom molecular dynamics simulations studying the partition of ions and the ionic current through the bacterial porin OmpF and two selected mutants. The study is motivated by new interesting experimental findings concerning their selectivity and conductance behaviour at neutral pH. The mutations considered here are designed to study the effect of removal of negative charges present in the constriction zone of the wild type OmpF channel (which contains on one side a cluster with three positive residues and on the other side two negatively charged residues). Our results show that these mutations induce an exclusion of cations from the constriction zone of the channel, substantially reducing the flow of cations. In fact, the partition of ions inside the mutant channels is strongly inhomogeneous, with regions containing excess of cations and regions containing excess of anions. Interestingly, the overall number of cations inside the channel is larger than the number of anions in the two mutants, as in the OmpF wild type channel. We found that the differences in ionic charge inside these channels are justified by the differences in electric charge between the wild type OmpF and the mutants, following an electroneutral balance.
Biophysical Journal, 2014
A distinctive feature of prokaryotic Na þ -channels is the presence of four glutamate residues in their selectivity filter. In this study, how the structure of the selectivity filter, and the free-energy profile of permeating Na þ ions are altered by the protonation state of Glu177 are analyzed. It was found that protonation of a single glutamate residue was enough to modify the conformation of the selectivity filter and its conduction properties. Molecular dynamics simulations revealed that Glu177 residues may adopt two conformations, with the side chain directed toward the extracellular entrance of the channel or the intracellular cavity. The likelihood of the inwardly directed arrangement increases when Glu177 residues are protonated. The presence of one glutamate residue with its chain directed toward the intracellular cavity increases the energy barrier for translocation of Na þ ions. These higher-energy barriers preclude Na þ ions to permeate the selectivity filter of prokaryotic Na þ -channels when one or more Glu177 residues are protonated.
Computational observation of an ion permeation through a channel protein
Bioscience reports, 1998
The ion permeation process, driven by a membrane potential through an outer membrane protein, OmpF porin of Escherichia coli, was simulated by molecular dynamics. A Na+ ion, initially placed in the solvent region at the outer side of the porin channel, moved along the electric field passing through the porin channel in a 1.3 nsec simulation; the permeation rate was consistent with the experimentally estimated channel activity (10(8)-10(9)/sec). It this simulation, it was indicated that the ion permeation through the porin channel proceeds by a "push-out" mechanism, and that Asp113 is an important residue for the channel activity.
On Conduction in a Bacterial Sodium Channel
PLoS Computational Biology, 2012
Voltage-gated Na + -channels are transmembrane proteins that are responsible for the fast depolarizing phase of the action potential in nerve and muscular cells. Selective permeability of Na + over Ca 2+ or K + ions is essential for the biological function of Na + -channels. After the emergence of the first high-resolution structure of a Na + -channel, an anionic coordination site was proposed to confer Na + selectivity through partial dehydration of Na + via its direct interaction with conserved glutamate side chains. By combining molecular dynamics simulations and free-energy calculations, a low-energy permeation pathway for Na + ion translocation through the selectivity filter of the recently determined crystal structure of a prokaryotic sodium channel from Arcobacter butzleri is characterised. The picture that emerges is that of a pore preferentially occupied by two ions, which can switch between different configurations by crossing low free-energy barriers. In contrast to K + -channels, the movements of the ions appear to be weakly coupled in Na + -channels. When the free-energy maps for Na + and K + ions are compared, a selective site is characterised in the narrowest region of the filter, where a hydrated Na + ion, and not a hydrated K + ion, is energetically stable.
Ion Binding Sites and Hydration in the Selectivity Filter of the Bacterial Sodium Channel Navab
Biophysical Journal, 2012
b S Supporting Information S odium is hydrated by either five (trigonal-bipyramidal) or six (octahedral) water molecules in crystal hydrate structures, whereas K + is hexa-coordinated. 1,2 In room-temperature concentrated salt solutions, neutron scattering data suggest that Na + coordination by water ranges from 4.8 to 5.3, whereas K + has slightly higher values but with a much less well-defined hydration shell. 3 Molecular simulations employing classical force fields are in fair agreement with these experimental findings for bulk hydration behavior. 4 The recently published structure 5,6 of a bacterial Na + ion channel (NavAb) in a closed-pore conformation with activated voltage sensors raises the question as to the nature of Na + (compared with K + ) coordination/hydration in the nanoscale confinement that is obtained in the lumen of an channel. The situation for voltage-gated K + (Kv) channels has been elucidated by numerous ingenious experiments as well as via molecular dynamics (MD) simulation. In brief, to pass through the Kv channel, K + ions must transit through a selectivity filter (SF) that is selective for K + over Na + by about 1000:1. 9À11 The narrow Kv-SF allows only single-file waters or K + ions and thus requires significant dehydration of the transiting ion. 10,12 In the preferred "knock on" mechanism, K + and waters alternate occupancy of four possible SF binding sites and move coherently when nudged by a K + that occupies a site external to the SF. 13À17 Typically, on passing the SF, K + has only two waters of hydration. The new crystal structure for NavAb suggests a much wider SF pore, which is consistent with the larger flux of Na + through Nav channels compared with K + through Kv channels. 5 Moreover, the Na + selectivity of NavAb over K + is only about 8:1. It is therefore of considerable interest to identify the Na + binding sites and to understand the hydration structures of Na + in Nav channels, which is the primary goal of the present MD simulations. The recent crystal structure of NavAb 5,6 offers a rare opportunity to make significant progress for the field.