Effect of flexibility on hydrophobic behavior of nanotube water channels

Andreev, Stefan A.; Reichman, David R.; Hummer, Gerhard

doi:10.1063/1.2104529

Cited by 77 publications

(61 citation statements)

References 60 publications

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“…Such features may be integral parts of the structure of proteins and other macromolecules, or they may appear fleetingly through conformational changes of a flexible molecule or surface, suggesting that flexible nonpolar surfaces ought to be more hydrophobic than rigid ones. This expectation is consistent with the results of Andreev et al (63), who showed that flexible nanotubes are more hydrophobic, expel water from their interior, and reduce the flow of water through them. Enhanced hydrophobicity as a result of flexibility should also influence water phase behavior and evaporation rates under nonpolar confinement.…”

Section: Discussionsupporting

confidence: 82%

Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

Venkateshwaran

et al. 2017

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

101

126

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Hydrophobic interactions drive many important biomolecular selfassembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute-water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.nanotube | curvature | chemical pattern | hydrophilicity | graphene H ydrophobic interactions drive many important biological and colloidal self-assembly processes (1-6). During such assembly, the hydration shells of the associating solutes are disrupted, replacing hydrophobic-water contacts with hydrophobic-hydrophobic ones. Characterizing how strongly water adheres to a given solute is, therefore, directly relevant to the strength of hydrophobic interactions between solutes. Macroscopically, surface-water adhesion is quantified by measuring the water droplet contact angle on a surface. However, such characterization does not translate usefully to proteins and other nanoscale solutes. Indeed, characterizing how strongly or weakly a protein surface or a specific patch on it adheres to water (i.e., its hydrophobicity) is incredibly challenging and has necessitated the use of simplifying assumptions.To this end, simple surface area (SA) models have been used to estimate the driving force for assembly, ∆G = γ∆A, where ∆A is the nonpolar SA buried upon assembly and γ is an appropriate surface tension (7-9). However, the value of γ used in popular models is nearly an order of magnitude lower t...

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Section: Discussionsupporting

confidence: 82%

Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

Venkateshwaran

et al. 2017

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

101

126

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“…40 In another scenario, the water in a highly occupied site cannot form its full complement of hydrogen bonds, 9,36 and it has been estimated that ejecting even a single such frustrated water molecule into the bulk can yield a biologically significant contribution to the free energy, up to several kilocalories per mole. 8,36,[41][42][43][44] Such phenomena are not accounted for well by continuum solvent models yet are important determinants of binding affinity.…”

Section: Introductionmentioning

confidence: 99%

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

Nguyen

Young²,

Gilson³

2012

The Journal of Chemical Physics

302

506

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The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a threedimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit [7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.

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“…Note that in both the lattice model and the atomistic simulations, the nanotube is assumed to be rigid. In previous simulation studies, the structure and dynamics of water inside nanotubes showed little sensitivity to the amplitude of wall fluctuations in artificially softened (6,6)-type tubes (32). Therefore, we do not expect a strong effect from the assumption of rigid nanotubes.…”

Section: Models and Methodsmentioning

confidence: 99%

Macroscopically ordered water in nanopores

Köfinger

Hummer

Dellago

2008

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

Self Cite

165

181

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Water confined into the interior channels of narrow carbon nanotubes or transmembrane proteins forms collectively oriented molecular wires held together by tight hydrogen bonds. Here, we explore the thermodynamic stability and dipolar orientation of such 1D water chains from nanoscopic to macroscopic dimensions. We show that a dipole lattice model accurately recovers key properties of 1D confined water when compared to atomically detailed simulations. In a major reduction in computational complexity, we represent the dipole model in terms of effective Coulombic charges, which allows us to study pores of macroscopic lengths in equilibrium with a water bath (or vapor). We find that at ambient conditions, the water chains filling the tube are essentially continuous up to macroscopic dimensions. At reduced water vapor pressure, we observe a 1D Ising-like filling/emptying transition without a true phase transition in the thermodynamic limit. In the filled state, the chains of water molecules in the tube remain dipole-ordered up to macroscopic lengths of Ϸ0.1 mm, and the dipolar order is estimated to persist for times up to Ϸ0.1 s. The observed dipolar order in continuous water chains is a precondition for the use of nanoconfined 1D water as mediator of fast long-range proton transport, e.g., in fuel cells. For water-filled nanotube bundles and membranes, we expect anti-ferroelectric behavior, resulting in a rich phase diagram similar to that of a 2D Coulomb gas.1D confinement ͉ antiferro-electric ͉ carbon nanotubes ͉ proton transfer ͉ phase transition T he 1D wires formed by water in molecularly narrow pores are central to the function of many biomolecules, offer new possibilities for technological applications, and provide model systems to study the unique properties of dimensionally confined fluids (1). Proteins filled by water wires, such as aquaporins and gramicidin A, mediate the transport of water, protons, or ions across biological membranes (2, 3). Inspired in part by biology, narrow water-filled pores have been suggested as promising building blocks for high-selectivity/high-flux membranes in molecular separation devices and fuel cells (4-8). As an example of the rich properties of nanoscopically confined fluids, 1D water wires in carbon nanotubes have been found to exhibit first-order like drying transitions (9).Carbon nanotubes provide nearly ideal systems to study water in 1D confinement. Their smooth interior cavity surface interacts in a relatively nonspecific way with water molecules, confining them to a narrow, almost cylindrical volume. In pores with subnanometer diameters, the water molecules arrange themselves in a single-file structure, linked by hydrogen bonds. Such ordered chains of water molecules were found to permit rapid water flow (4, 9), and mediate proton transfer with mobilities exceeding those in bulk water (10-13).A key factor for the unique properties of 1D confined water is the nearly perfect molecular order, both translationally and orientationally, with uninterrupted chains of wate...

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Effect of flexibility on hydrophobic behavior of nanotube water channels

Cited by 77 publications

References 60 publications

Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

Macroscopically ordered water in nanopores

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