Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Number of Citing Articles: 5 new records this week (5 in this e-mail)
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Title:
Boron Nitride Nanotubes Selectively Permeable to Cations or Anions
Authors:
Hilder, TA; Gordon, D; Chung, SH
Author Full Names:
Hilder, Tamsyn A.; Gordon, Daniel; Chung, Shin-Ho
Source:
SMALL 5 (24): 2870-2875 DEC 4 2009
Language:
English
Document Type:
Article
Author Keywords:
engineered ion channels; ion selectivity; membranes; molecular dynamics; nanotubes
KeyWords Plus:
CARBON NANOTUBE; MOLECULAR-DYNAMICS; BROWNIAN DYNAMICS; WATER; TRANSPORT; PERMEATION; MEMBRANES; ENERGY; FUNCTIONALIZATION; CONDUCTION
Abstract:
Biological ion channels in membranes are selectively permeable to specific ionic species. They maintain the resting membrane potential, generate propagated action potentials, and control a wide variety of cell functions. Here it is demonstrated theoretically that boron nitride nanotubes have the ability to carry out some of the important functions of biological ion channels. Boron nitride nanotubes with radii of 4.83 and 5.52 angstrom embedded in a silicon nitride membrane are selectively permeable to cations and anions, respectively. They broadly mimic some of the permeation characteristics of gramicidin and chloride channels. Using distributional molecular dynamics, which is a combination of molecular and stochastic dynamics simulations, the properties of these engineered nanotubes are characterized, such as the free energy encountered by charged particles, the water-ion structure within the pore, and the current-voltage and current-concentration profiles. These engineered!
nanotubes have potential applications as sensitive biosensors, antibiotics, or filtration devices.
Reprint Address:
Hilder, TA, Australian Natl Univ, Res Sch Biol, Computat Biophys Grp, GPO Box 4, Canberra, ACT 2601, Australia.
Research Institution addresses:
[Hilder, Tamsyn A.; Gordon, Daniel; Chung, Shin-Ho] Australian Natl Univ, Res Sch Biol, Computat Biophys Grp, Canberra, ACT 2601, Australia
E-mail Address:
tamsyn.hilder@anu.edu.au
Cited References:
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Cited Reference Count:
44
Times Cited:
0
Publisher:
WILEY-V C H VERLAG GMBH; PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY
Subject Category:
Chemistry, Multidisciplinary; Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter
ISSN:
1613-6810
DOI:
10.1002/smll.200901229
IDS Number:
541JV
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Title:
Influence of endohedral water on diameter sorting of single-walled carbon nanotubes by density gradient centrifugation
Authors:
Quintilla, A; Hennrich, F; Lebedkin, S; Kappes, MM; Wenzel, W
Author Full Names:
Quintilla, A.; Hennrich, F.; Lebedkin, S.; Kappes, Manfred M.; Wenzel, Wolfgang
Source:
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12 (4): 902-908 2010
Language:
English
Document Type:
Article
KeyWords Plus:
MOLECULAR-DYNAMICS; SIMULATIONS; BEHAVIOR; GROMACS
Abstract:
Separation of single-walled carbon nanotubes (SWNT) by diameter is an important prerequisite for controlled experimental studies and efficient application of these systems. By comparing experimental data with molecular dynamics (MD) simulations, we demonstrate that water filling has a significant, tube-diameter dependent effect on the effective mass density of individual single-walled carbon nanotubes suspended in aqueous surfactant suspensions. We present a model for the effective density of the nanotube-surfactant complex in aqueous solution that permits a comprehensive description of its density across the entire, experimentally relevant range of SWNT diameters. Parameters for this model can be obtained from molecular dynamics simulations and/or experiment and help explain the subtle interplay of surfactant coverage and endohedral water in the separation of a particular diameter species of SWNT by gradient centrifugation.
Reprint Address:
Wenzel, W, Forschungszentrum Karlsruhe, Inst Nanotechnol, D-76021 Karlsruhe, Germany.
Research Institution addresses:
[Quintilla, A.; Hennrich, F.; Lebedkin, S.; Kappes, Manfred M.; Wenzel, Wolfgang] Forschungszentrum Karlsruhe, Inst Nanotechnol, D-76021 Karlsruhe, Germany; [Kappes, Manfred M.] Univ Karlsruhe, Inst Phys Chem, D-76128 Karlsruhe, Germany; [Kappes, Manfred M.; Wenzel, Wolfgang] Univ Karlsruhe, DFG Zentrum Funkt Nanostrukturen, D-76131 Karlsruhe, Germany
E-mail Address:
wolfgang.wenzel@kit.edu
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34
Times Cited:
0
Publisher:
ROYAL SOC CHEMISTRY; THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND
Subject Category:
Chemistry, Physical; Physics, Atomic, Molecular & Chemical
ISSN:
1463-9076
DOI:
10.1039/b912847f
IDS Number:
542TB
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Title:
Molecular Modeling of Two Distinct Triangular Oligomers in Amyloid beta-protein
Authors:
Zheng, J; Yu, X; Wang, JD; Yang, JC; Wang, QM
Author Full Names:
Zheng, Jie; Yu, Xiang; Wang, Jingdai; Yang, Jui-Chen; Wang, Qiuming
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (1): 463-470 JAN 14 2010
Language:
English
Document Type:
Article
KeyWords Plus:
ALZHEIMERS A-BETA(1-40) PEPTIDE; DYNAMICS SIMULATIONS; FIBRIL ELONGATION; ATOMIC STRUCTURES; COMMON MECHANISM; ION CHANNELS; DISEASE; A-BETA(17-42); POLYMORPHISM; PATHOGENESIS
Abstract:
Arnyloid-beta (A beta) peptides exhibit many distinct structural morphology at the early aggregate stage, some of which are biological relevant to the pathogenesis of Alzheimer's disease (AD). Atomic-resolution structures of the early A beta aggregates and their conformational changes in amyloid aggregation remain elusive. Here, we perform all-atom molecular modeling and dynamics simulations to obtain two stable triangular-like A beta structures with the lowest packing energy, one corresponding to the Tycko's model (Paravastu, A.; Leapman, R.; Yau, W.; Tycko, R. Proc. Nat. Acad. Soc. U.S.A. 2008, 105, 18349-18354) (referred to C-WT model) and the other corresponding to computational model (N-WT model). Both models have the same 3-fold symmetry but distinct beta-sheet organizations in which three A beta hexamers pack together via either C-terminal beta-strand residues or N-terminal beta-strand residues forming distinct hydrophobic cross section. Structural and energetic compa!
risons of two 3-fold A beta oligomers, coupled with Structural changes upon the mutations Occurring at the interacting interfaces, reveal that although hydrophobic interactions are still dominant forces, electrostatic interactions are more favorable in the N-WT model due to the formation of more and stable intersheet salt bridges, while solvation energy is more favorable in the C-WT model due to more exposed hydrophilic residues to solvent. Both models display many common features similar to other amyloid oligomers and therefore are likely to be biologically relevant.
Reprint Address:
Zheng, J, Univ Akron, Dept Chem & Biomol Engn, Akron, OH 44325 USA.
Research Institution addresses:
[Zheng, Jie; Yu, Xiang; Yang, Jui-Chen; Wang, Qiuming] Univ Akron, Dept Chem & Biomol Engn, Akron, OH 44325 USA; [Wang, Jingdai] Zhejiang Univ, Dept Chem Engn, Hangzhou 310027, Zhejiang, Peoples R China
E-mail Address:
zhengj@uakron.edu
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50
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp907608s
IDS Number:
541GY
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Title:
Higher Susceptibility to Halothane Modulation in Open- Than in Closed-Channel alpha 4 beta 2 nAChR Revealed by Molecular Dynamics Simulations
Authors:
Liu, LT; Haddadian, EJ; Willenbring, D; Xu, Y; Tang, P
Author Full Names:
Liu, Lu Tian; Haddadian, Esmael J.; Willenbring, Dan; Xu, Yan; Tang, Pei
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (1): 626-632 JAN 14 2010
Language:
English
Document Type:
Article
KeyWords Plus:
NICOTINIC ACETYLCHOLINE-RECEPTOR; LIGAND-BINDING DOMAIN; NORMAL-MODE ANALYSIS; GATED ION CHANNELS; GENERAL-ANESTHETICS; GABA(A) RECEPTOR; AGONIST BINDING; VOLATILE ANESTHETICS; GATING MECHANISM; IDENTIFICATION
Abstract:
The neuronal alpha 4 beta 2 nicotinic acetylcholine receptor (nAChR) is a potential molecular target for general anesthetics. It is unclear, however, whether anesthetic action produces the same effect oil the open and closed channels. Computations parallel to Our previous open channel Study (J. Phys. Chem. B 2009, 113, 12581) were performed oil the closed-channel alpha 4 beta 2 nAChR to investigate the conformation-dependent anesthetic effects oil channel Structures and dynamics. Flexible ligand docking and over 20 ns molecular dynamics simulations revealed similar halothane-binding sites in the closed and open channels. The sites with relatively high binding affinities (similar to -6.0 kcal/mol) were identified at the interface of extracellular (EC) and transmembrane (TM) domains or at the interface between alpha 4 and beta 2 Subunits. Despite similar sites for halothane binding, the closed-channel conformation showed much less sensitivity than the open channel to the struc!
tural and dynamical perturbations from halothane. Compared to the systems Without anesthetics, the amount of water inside the pore decreased by 22% in the presence of halothane in the open channel but only by 6% in the closed channel. Comparison of the nonbonded interactions at the EC/TM interfaces suggested that the beta 2 Subunits were more prone than the alpha 4 subunits to halothane binding. In addition, our data Support the notion that halothane exerts its effect by disturbing the quaternary structure and dynamics of the channel. The study Concludes that sensitivity and global dynamics responsiveness of alpha 4 beta 2 nAChR to halothane are conformation dependent. The effect of halothane on the global dynamics of the open-channel conformation might also account for the action of other inhaled general anesthetics.
Reprint Address:
Tang, P, Univ Pittsburgh, Sch Med, Dept Anesthesiol, 2049 Biomed Sci Tower 3,3501 5th Ave, Pittsburgh, PA 15261 USA.
Research Institution addresses:
[Liu, Lu Tian; Haddadian, Esmael J.; Willenbring, Dan; Xu, Yan; Tang, Pei] Univ Pittsburgh, Sch Med, Dept Anesthesiol, Pittsburgh, PA 15261 USA; [Xu, Yan; Tang, Pei] Univ Pittsburgh, Sch Med, Dept Pharmacol & Chem Biol, Pittsburgh, PA 15261 USA; [Xu, Yan] Univ Pittsburgh, Sch Med, Dept Biol Struct, Pittsburgh, PA 15261 USA; [Tang, Pei] Univ Pittsburgh, Sch Med, Dept Computat Biol, Pittsburgh, PA 15261 USA
E-mail Address:
tangp@anes.upmc.edu
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Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp908944e
IDS Number:
541GY
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Title:
Controllable Synthetic Molecular Channels: Biomimetic Ammonia Switch
Authors:
Titov, AV; Wang, BY; Sint, K; Kral, P
Author Full Names:
Titov, Alexey V.; Wang, Boyang; Sint, Kyaw; Kral, Petr
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (2): 1174-1179 JAN 21 2010
Language:
English
Document Type:
Article
KeyWords Plus:
FUNCTIONALIZED CARBON NANOTUBES; AQUAPORIN WATER CHANNELS; ION CHANNELS; DYNAMICS SIMULATIONS; PEPTIDE NANOTUBES; FLOWING LIQUIDS; GAS SEPARATION; K+ CHANNEL; PROTEIN; DESIGN
Abstract:
We use molecular dynamics simulations combined with iterative screening to test if one can design mechanically controllable and selective molecular pores. The first model pore is formed by two stacked carbon nanocones connected by aliphatic chains at their open tips, in analogy to aquaporins. It turns out that when one nanocone is gradually rotated with respect to the other, the molecular chains alter the size of the nanopore formed at the cone tips and control the flow rates of liquid pentane through it. The second model pore is formed by two carbon nanotubes joined by a cylindrical structure of antiparallel peptides. By application of a torque to one of the nanotubes, while holding the other, we can reversibly fold the peptides into forward or backward-twisted barrels. We have modified the internal residues in these barrels to make these pores selective and controllable. Eventually, we found a nanopore that in the two folded configurations has very different transmission r!
ates for hydrated NH3 molecules.
Reprint Address:
Kral, P, Univ Illinois, Dept Chem, Chicago, IL 60607 USA.
Research Institution addresses:
[Titov, Alexey V.; Wang, Boyang; Sint, Kyaw; Kral, Petr] Univ Illinois, Dept Chem, Chicago, IL 60607 USA
E-mail Address:
pkral@uic.edu
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0
Publisher:
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Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp9103933
IDS Number:
541HD
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