Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Molecular dynamics investigation of hydration of nanoscopic hydrophobic paraffin-like plates
Authors:
Choudhury, N
Author Full Names:
Choudhury, Niharendu
Source:
JOURNAL OF CHEMICAL PHYSICS 131 (1): Art. No. 014507 JUL 7 2009
Language:
English
Document Type:
Article
Author Keywords:
hydrogen bonds; hydrophobicity; molecular dynamics method; molecular moments; molecular orientation; plates (structures); solvation; water; wetting
KeyWords Plus:
DEWETTING TRANSITION; HYDROPHILIC SURFACES; CARBON NANOTUBES; LIQUID WATER; SOLUTE SIZE; SIMULATION; COLLAPSE; C-60; INTERFACES; NANOSCALE
Abstract:
The effect of surface characteristics on the hydration behavior of various paraffin-like plates has been investigated. Structure and orientation characteristics of the water molecules in the solvation shells of various nanoscopic paraffin-like plates differing from each other in the intermolecular spacing have been extensively studied using molecular dynamics simulation in isothermal-isobaric ensemble. Single particle density distribution of water molecules around the plate reveals well defined solvation shells around each of the paraffin-like plates studied here. A sharp first peak in the density profile in each of the plates signifies no visible dewetting around the paraffin plate. Instantaneous density of water molecules around the plate also reveals that the plate is sufficiently hydrated and there is no intermittent fluctuation in water density in the first hydration shell leading to short lived dewetted state for any of the model plates within the two nanosecond time s!
pan. This is in contrast to the hydration behavior of the intersolute region, where intersolute dewetting has been observed for some of the model plates. Thus the present results demonstrate that dewetting in the intersolute region of nanoscopic hydrophobic plates does not stem from drying interface of the individual solute. No significant effect of surface topology on the orientational structure of water molecules as revealed through distributions of dipole moment as well as oxygen-hydrogen bond vectors of a water molecule in different solvation shells has been observed.
Reprint Address:
Choudhury, N, Bhabha Atom Res Ctr, Theoret Chem Sect, Chem Grp, Bombay 400085, Maharashtra, India.
Research Institution addresses:
Bhabha Atom Res Ctr, Theoret Chem Sect, Chem Grp, Bombay 400085, Maharashtra, India
E-mail Address:
nihcho@barc.gov.in
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Cited Reference Count:
51
Times Cited:
0
Publisher:
AMER INST PHYSICS; CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA
Subject Category:
Physics, Atomic, Molecular & Chemical
ISSN:
0021-9606
DOI:
10.1063/1.3155186
IDS Number:
468EY
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Title:
Proton Transport Pathway in the CIC Cl-/H+ Antiporter
Authors:
Wang, D; Voth, GA
Author Full Names:
Wang, Dong; Voth, Gregory A.
Source:
BIOPHYSICAL JOURNAL 97 (1): 121-131 JUL 8 2009
Language:
English
Document Type:
Article
KeyWords Plus:
VALENCE-BOND MODEL; CHLORIDE CHANNELS; COMPUTER-SIMULATION; EXCHANGE TRANSPORTER; BIOMOLECULAR SYSTEMS; PROKARYOTIC HOMOLOG; ESCHERICHIA-COLI; SIDE-CHAIN; WATER; PROTEINS
Abstract:
A fundamental question concerning the CIC Cl-/H+ antiporters is the nature of their proton transport (PT) pathway, We addressed this issue by using a novel computational methodology capable of describing the explicit PT dynamics in the CIC-ec1 protein. The main result is that the Glu(203) residue delivers a proton from the intracellular solution to the core of CIC-ec1 via a rotation of its side chain and subsequent acid dissociation. After reorientation of the Glu(203) side chain, a transient water-mediated PT pathway between Glu(203) and Glu(148) is established that is able to receive and translocate the proton via Grotthuss shuttling after deprotonation of Glu(203). A molecular-dynamics simulation of an explicit hydrated excess proton in this pathway suggests that a negatively charged Glu(148) and the central Cl- ion act together to drive H+ to the extracellular side of the membrane. This finding is consistent with the experimental result that Cl- binding to the central si!
te facilitates the proton movement. A calculation of the PT free-energy barrier for the CIC-ec1 E203V mutant also supports the proposal that a dissociable residue is required at this position for efficient delivery of H+ to the protein interior, in agreement with recent experimental results.
Reprint Address:
Voth, GA, Univ Utah, Ctr Biophys Modeling & Simulat, Salt Lake City, UT 84112 USA.
Research Institution addresses:
[Voth, Gregory A.] Univ Utah, Ctr Biophys Modeling & Simulat, Salt Lake City, UT 84112 USA; Univ Utah, Dept Chem, Salt Lake City, UT 84112 USA
E-mail Address:
voth@chem.utah.edu
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Cited Reference Count:
52
Times Cited:
0
Publisher:
CELL PRESS; 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA
Subject Category:
Biophysics
ISSN:
0006-3495
DOI:
10.1016/j.bpj.2009.04.038
IDS Number:
469BV
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