Water diffusion through a membrane protein channel: A first passage time approach

Abstract

Water diffusion through OmpF, a porin in the outer membrane of Escherichia coli, is studied by molecular dynamics simulation. A first passage time approach allows characterizing the diffusive properties of a well-defined region of this channel. A carbon nanotube, which is considerably more homogeneous, serves as a model to validate the methodology. Here we find, in addition to the expected regular behavior, a gradient of the diffusion coefficient at the channel ends, witness of the transition from confinement in the channel to bulk behavior in the connected reservoirs. Moreover, we observe the effect of a kinetic boundary layer, which is the counterpart of the initial ballistic regime in a mean square displacement analysis. The overall diffusive behavior of water in OmpF shows remarkable similarity with that in a homogeneous channel. However, a small fraction of the water molecules appears to be trapped by the protein wall for considerable lengths of time. The distribution of trapping times exhibits a broad power law distribution ͑ ͒ϳ −2.4 , up to = 10 ns, a bound set by the length of the simulation run. We discuss the effect of this distribution on the dynamic properties of water in OmpF in terms of incomplete sampling of phase space.

Thermophoretic Motion of Water Nanodroplets Confined inside Carbon Nanotubes

“…This value is in reasonable agreement with values previous obtained for water under nanoscale confinement (D ) 0.94-5.7 nm 2 /ns). [41][42][43] For the simulations with a nonzero thermal gradient, we observe a linear increase in the center of mass velocity as function of the thermal gradient (Figure 5a) which confirms that the motion is thermophoretic. We expect that the motion is related to high-frequency phonon vibrations of the carbon nanotubes, i.e., the kinetic pressure of the carbon nanotubes as demonstrated in ref 21.…”

First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin

“…(3)- (5), the interval length L needs to be considered slightly longer than its actual length in the MD simulations [27]. This extra distance, which appears to be dependent on the type of particle and the interval, has been studied and identified before as the Milne extrapolation length [27,39].…”

“…(1) and (2). To circumvent that limitation, Hijkoop et al [27], inspired by the work of Munakata and Kaneko [28], used a method based on a first-passage-time (FPT) analysis to compute a global diffusion coefficient of water in the interior of an artificial (uncharged) OmpF porin. Their analysis, however, ignores the influence of free-energy barriers and wells on the local movements of water molecules at a specific position along the axis of the pore.…”

“…This procedure allows us to obtain the effective diffusion coefficients of the ions in the channel from all-atom MD simulations [27,29,30]. On the one hand, from the trajectories of the ions provided by the simulations one can calculate several FPT quantities that characterize their passage through the channel.…”

Diffusion at the liquid-vapor interface

“…[13][14][15]21 Surfactants will be usually located at the surface and most will reach the diffusive regime. The relationship between structure and dynamics is specially interesting in systems with strong profiling, such as liquid metals, 20 confined water, 22,23,25,27,28 and liquid-solid interfaces. 29 Similarly, diffusion in amphiphilic bilayer structures, 24,25 micelles, 26 and microemulsions can be described in a manner similar to the one presented here.…”