Carbon Nanotube Based Artificial Water Channel Protein: Membrane Perturbation and Water Transportation

Liu, Bo; Li, Xiaohua; Li, Baolei; Xu, Bingqian; Zhao, Yuliang

doi:10.1021/nl8030339

Cited by 106 publications

(99 citation statements)

References 68 publications

(108 reference statements)

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“…This mechanism depends critically upon the degree of flexibility of the pore lining side chains. This blueprint may provide a new design principle, for example, derivatization of nanopores (24) to form ion selective biomimetic channels. Furthermore, an improved understanding may aid design of selective blockers of OprP to aid in fighting Pseudomonas infection.…”

Section: Discussionmentioning

confidence: 99%

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

Pongprayoon

Beckstein

Wee

et al. 2009

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

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The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of Ϸ8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 M is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a ''charged brush'' to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl ؊ PMF. The difference in affinity and hence selectivity is due to the ''Lys-cluster'' motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl ؊ by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.free energy profile ͉ potential of mean force ͉ anion selectivity ͉ hydration ͉ molecular dynamics simulation

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Section: Discussionmentioning

confidence: 99%

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

Pongprayoon

Beckstein

Wee

et al. 2009

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

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“…[2][3][4] Carbon nanotubes (CNTs) have attracted great interest from both scientists and the industry because their high aspect ratios, strength and remarkable physical properties make them a unique material with a wide range of promising applications. Many applications of CNTs in biomedicine have been proposed, including nanoelectronics, 4 biosensors, 5 biomolecular recognition devices and molecular transporters, 6 artificial water channels, 7 cancer therapy 8,9 and photoacoustic molecular imaging. 10 Because transitional metals are often used as catalysts during CNT synthesis, 11 it is unavoidable that as-received CNTs are contaminated by catalyst residues.…”

Section: Introductionmentioning

confidence: 99%

The contributions of metal impurities and tube structure to the toxicity of carbon nanotube materials

et al. 2012

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Due to the existence of considerable quantities of metallic and carbonaceous impurities, the key factor and mechanism for the reported toxicity of carbon nanotubes (CNTs) are unclear. Here, we first quantify the contribution of metal residues and fiber structure to the toxicity of CNTs. Significant quantities of metal particles could be mobilized from CNTs into surrounding fluids, depending on the properties and constituents of the biological microenvironment, as well as the properties of metal particles. Furthermore, electron spin resonance measurements confirm that hydroxyl radicals can be generated by both CNTs containing metal impurities and acid-leachable metals from CNTs. Several biomolecules facilitate the generation of free radicals, which might be due to the participation of these biomolecules in redox cycling influenced by pH. Among several major metal residues, Fe has a critical role in generating hydroxyl radicals, reducing cell viability and promoting intracellular reactive oxidative species. Cell viability is highly dependent on the amount of metal residues and iron in particular, but not tube structure, while the negative effect of CNTs themselves on cell viability is very limited in a certain concentration range below 80 lg ml À1 . It is crucial to systematically understand how these exogenous and endogenous factors influence the toxicity of CNTs to avoid their undesirable toxicity. Keywords: biological microenvironments; carbon nanotube; metal impurities; reactive oxygen species; toxicity INTRODUCTION Engineered nanomaterials possess novel properties and have been used worldwide in numerous consumer products, for example, food, clothes, pharmaceuticals and cleaning products. Estimates suggest that by 2015 nanotechnology will have a trillion-plus dollar global economic impact. 1 Therefore, ensuring the safety of nanomaterials is of great importance to the tremendous commercial applications of nanotechnology. Safety evaluation of nanomaterials should consider their behaviors in various aspects, including their interaction with proteins, DNA, lipids, membranes, organelles, cells, tissues, biological fluids and even the dissolution of metal constituents. [2][3][4] Carbon nanotubes (CNTs) have attracted great interest from both scientists and the industry because their high aspect ratios, strength and remarkable physical properties make them a unique material with a wide range of promising applications. Many applications of CNTs in biomedicine have been proposed, including nanoelectronics, 4 biosensors, 5 biomolecular recognition devices and molecular transporters, 6 artificial water channels, 7 cancer therapy 8,9 and photoacoustic molecular imaging. 10 Because transitional metals are often used as catalysts during CNT synthesis, 11 it is unavoidable that as-received CNTs are contaminated by catalyst residues. 12 The catalyst precursor (such as iron carbonyl) decomposes, and nanometer-sized metal particles form from the decomposition products. Therefore,

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“…However, the modified base engenders even higher ion current than the normal DNA strand. In order to study the mechanism of CNT-based nanopore function and the seemingly abnormal behavior of ion current in the presence of Bzim-modified DNA, we first calculate the potential of mean force (PMF) 52 In addition, we calculate the axial distribution of ssDNA and study the possible impact of DNA distribution on the ion distribution and the concomitant ion transport (Figure 3c, d). The CNT with a length of 48 Å can accommodate DNA segments of around ten nucleotides.…”

Section: Resultsmentioning

confidence: 99%

Sensitive Detection of a Modified Base in Single-Stranded DNA by a Single-Walled Carbon Nanotube

et al. 2015

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In this work, we use molecular dynamics simulations to study the responses of the configuration of single-strand DNA (ssDNA) within a carbon nanotube (CNT) and the concomitant ion flow to a single modified base, i.e., benzoimidazole (Bzim)-modified 5-hydroxymethyl cytosine (5hmC). Our simulation results show the Bzim-modified 5hmC can considerably increase the ion flow through a single-walled carbon nanotube (SWCNT), despite its larger size, which is consistent with prior experimental results. This phenomenon is attributed to enhanced adsorption of DNA to the interior wall of the CNT driven by the Bzim-modified 5hmC, leading to a reduced steric effect on ion transport through the CNT. As revealed in this work, the distribution of ssDNA can be affected by limited change in the interactions with the CNT surface. Such behavior of ssDNA within small-sized CNTs can be exploited to further improve the sensitivity of nanopore detection.

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Carbon Nanotube Based Artificial Water Channel Protein: Membrane Perturbation and Water Transportation

Cited by 106 publications

References 68 publications

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate

The contributions of metal impurities and tube structure to the toxicity of carbon nanotube materials

Sensitive Detection of a Modified Base in Single-Stranded DNA by a Single-Walled Carbon Nanotube

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