Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes

Cao, Zhen; Peng, Yuxing; Yan, Tianying; Shu, Li; Li, Ailin; Voth, Gregory A.

doi:10.1021/ja1046704

Cited by 150 publications

(179 citation statements)

References 21 publications

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“…For instance, compared with K + conductance that requires physical diffusion, proton transport could be much more efficient based on an orientational hydrogen-bonding defect mechanism 50,51 . Here the observed K + /Na + selectivity can be understood based on conclusions from previous MD simulations 48,49 , which demonstrates that the free-energy costs of constraining hydrated K + within a sub-nm pore are notably less than those of hydrated Na + .…”

Section: Discussionmentioning

confidence: 99%

Self-assembling subnanometer pores with unusual mass-transport properties

et al. 2012

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A long-standing aim in molecular self-assembly is the development of synthetic nanopores capable of mimicking the mass-transport characteristics of biological channels and pores. Here we report a strategy for enforcing the nanotubular assembly of rigid macrocycles in both the solid state and solution based on the interplay of multiple hydrogen-bonding and aromatic π − π stacking interactions. The resultant nanotubes have modifiable surfaces and inner pores of a uniform diameter defined by the constituent macrocycles. The self-assembling hydrophobic nanopores can mediate not only highly selective transmembrane ion transport, unprecedented for a synthetic nanopore, but also highly efficient transmembrane water permeability. These results establish a solid foundation for developing synthetically accessible, robust nanostructured systems with broad applications such as reconstituted mimicry of defined functions solely achieved by biological nanostructures, molecular sensing, and the fabrication of porous materials required for water purification and molecular separations.

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Section: Discussionmentioning

confidence: 99%

Self-assembling subnanometer pores with unusual mass-transport properties

et al. 2012

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“…In this context, ion channels present the greatest challenges and opportunities: Their narrow pores are usually hydrated; thus, channel blockers effectively have to displace these pore waters. Particularly compelling in this regard are proton channels, such as the M2 proton channel of influenza A virus and Hv1, because waters represent the vehicle with which to achieve proton conduction (91)(92)(93)(94)(95)(96). Notably, in the case of M2, the drug amantadine and other hydrophobic scaffolds were shown to displace clusters of hydrogenbonded waters from main hydration sites (52,54).…”

Section: S1mentioning

confidence: 99%

On the role of water density fluctuations in the inhibition of a proton channel

Gianti

Delemotte

Klein

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.Hv1 | drug design | pore waters | binding site discovery | confined waters

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“…Recently, a work based on multi-state empirical valence bond (EVB) calculations on PT in one-dimensional water chains confined in carbon nanotubes confirmed early results from Hummer et al [29] and revealed that the rate of PT inside the tubes was one order of magnitude faster than in bulk. [28] On the other hand, ab-initio molecular dynamics simulations of water inside nanotube channels [29][30][31] have revealed different mobilities for hydroxide and hydronium ions inside the tubes, depending on the size of the tube and the degree of functionalization of the tube walls. A very recent work [32] reports proton transfer within graphene layers when surrounded by water.…”

Section: Introductionmentioning

confidence: 99%

Proton transfer in liquid water confined inside graphene slabs

Tahat

Martı́

2015

Phys. Rev. E

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The microscopic structure and dynamics of an excess proton in water constrained in narrow graphene slabs between 0.7 and 3.1 nm wide has been studied by means of a series of molecular dynamics simulations. Interaction of water and carbon with the proton species was modelled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of confinement on proton solvation structure and on its dynamical properties has been considered for varying densities. The system is organized in one interfacial and a bulk-like region, both of variable size.In the widest interplate separations, the lone proton shows a marked tendency to place itself in the bulk phase of the system, due to the repulsive interaction with the carbon atoms. However, as the system is compressed and the proton is forced to move to the vicinity of graphene walls it moves closer to the interface, producing a neat enhancement of the local structure. We found a marked slowdown of proton transfer when the separation of the two graphene plates is reduced. In the case of lowest distances between graphene plates (0.7 and 0.9 nm), only one-two water layers persist and the two-dimensional character of water structure becomes evident. By means of spectroscopical analysis, we observed the persistence of Zundel and Eigen structures in all cases, although at low interplate separations a signature frequency band around 2500 cm −1 suffers a blue-shift and moves to characteristical values of asymmetric hydronium ion vibrations, indicating some unstability of the typical Zundel-Eigen moieties and their eventual conversion to a single hydronium species solvated by water.

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Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes

Cited by 150 publications

References 21 publications

Self-assembling subnanometer pores with unusual mass-transport properties

Self-assembling subnanometer pores with unusual mass-transport properties

On the role of water density fluctuations in the inhibition of a proton channel

Proton transfer in liquid water confined inside graphene slabs

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