[show abstract][hide abstract] ABSTRACT: The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss shuttling) proton and a classical (nonshuttling) hydronium ion along two aquaporin channels, Aqp1 and GlpF. To elucidate the effects of the bipolar field thought to arise from two alpha-helical macrodipoles on proton blockage, free energy profiles were also calculated for computational mutants of the two channels where the bipolar field was eliminated by artificially discharging the backbone atoms. Comparison of the free energy profiles between the proton and hydronium cases indicates that the magnitude of the free energy barrier and position of the barrier peak for the fully delocalized and shuttling proton are somewhat different from the case of the (localized) classical hydronium. The proton conductance through the two aquaporin channels is also estimated using Poisson-Nernst-Planck theory for both the Grotthuss shuttling excess proton and the classical hydronium cation.
[show abstract][hide abstract] ABSTRACT: Water translocation between various compartments of a system is a fundamental process in biology of all living cells and in
a wide variety of technological problems. The process is of interest in different fields of physiology, physical chemistry,
and physics, and many scientists have tried to describe the process through physical models. Owing to advances in computer
simulation of molecular processes at an atomic level, water transport has been studied in a variety of molecular systems ranging
from biological water channels to artificial nanotubes. While simulations have successfully described various kinetic aspects
of water transport, offering a simple, unified model to describe trans-channel translocation of water turned out to be a nontrivial
[show abstract][hide abstract] ABSTRACT: Water permeation through nanometric channels, generally a coupled many-body process, is described in this study by a single collective coordinate. A collective diffusion model is proposed in which water movement at equilibrium is characterized as an unbiased diffusion along this coordinate and water transport in the presence of a chemical potential difference is described as one-dimensional diffusion in a linear potential. The model allows one to determine the osmotic permeability of a water channel from equilibrium simulations.
[show abstract][hide abstract] ABSTRACT: We discuss the difference between osmotic permeability pf and diffusion permeability pd of single-file water channels and demonstrate that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While pd can be directly obtained from equilibrium molecular dynamics simulations, pf can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which pf can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated pf of 7.1 x 10(-14) cm(3)/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that pf/pd for aquaporin-1 measures approximately 12. This number is explained in terms of channel architecture and conduction mechanism.
[show abstract][hide abstract] ABSTRACT: Carbon nanotubes, unmodified (pristine) and modified through charged atoms, were simulated in water, and their water conduction rates determined. The conducted water inside the nanotubes was found to exhibit a strong ordering of its dipole moments. In pristine nanotubes the water dipoles adopt a single orientation along the tube axis with a low flipping rate between the two possible alignments. Modification can induce in nanotubes a bipolar ordering as previously observed in biological water channels. Network thermodynamics was applied to investigate proton conduction through the nanotubes.
[show abstract][hide abstract] ABSTRACT: A method is proposed to measure the water permeability of membrane channels by means of molecular dynamics simulations. By applying a constant force to the bulk water molecules and a counter force on the complementary system, a hydrostatic pressure difference across the membrane can be established, producing a net directional water flow. The hydraulic or osmotic permeability can then be determined by the ratio of the water flux and the pressure difference. The method is applied and tested on an aquaglyceroporin channel through a series of simulations totaling 5 ns in duration.
[show abstract][hide abstract] ABSTRACT: The aquaporin-1 water channel was modeled in a palmitoyl-oleoyl-phosphatidyl-choline lipid bilayer, by means of molecular dynamics simulations. Interaction of the protein with the membrane and inter-monomer interactions were analyzed. Structural features of the channel important for its biological function, including the Asn-Pro-Ala (NPA) motifs, and the diffusion of water molecules into the channels, were investigated. Simulations revealed the formation of single file water inside the channels for certain relative positions of the NPA motifs.